# BASIC 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
-->

<!--

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)

-->

format-version:
date:
saved-by:
auto-generated-by:
subsetdef: PSI-ID_slim "Subset of PSI-ID"
synonymtypedef: PSI-ID-alternate "Alternate label curated by PSI-ID" EXACT
synonymtypedef: PSI-ID-short "Unique short label curated by PSI-ID" EXACT
default-namespace: PSI-ID
remark: Notes:
remark: Each of the top level terms in this file is the root term of an independent controlled vocabulary
remark: mapping an element of the PSI Intrinsic Disorder XML schema.
remark: coverage: This file collects controlled vocabularies describing different aspects of intrinsically disordered proteins.
remark: publisher: This file is published by the PSI-ID working group, see http://psidev.info/ID
remark: CVversion: 1.0.0
ontology: id or idp or idpo

<!-- ROOT TERM -->

[Term]
id: ID:0000 or IDP:0000 or IDPO:0000 ?
name: intrinsic disorder or intrinsically disordered protein(s) or something with ontology ?
def: "Controlled vocabularies created for intrinsically disordered proteins." [PMID:31824649]
subset: PSI-ID_slim ?
synonym: "id" or "idp" EXACT PSI-ID-short [] ?
created_by: ?
creation_date: ?

<!-- ALIAS TYPE - ROOT TERM FOR NAME ELEMENT ANNOTATION - type and typeAc attributes of idf:alias elements to annotate free text stored as value of these elements -->

[Term]
id:
name: alias type
def: "Descriptor of the type of nomenclature used to describe an object or an entity." [PMID:31824649]
relationship: part_of ID:0000 ! intrinsically disordered protein

[Term]
id:
name: synonym
def: "Alternative name or descriptor for an object or an entity." [PMID:31824649]
is_a: ??:xxxx ! alias type

[Term]
id:
name: author assigned name
def: "Name assigned to an object or entity by the authors within a paper that may differ from the name used in a reference database." [PMID:31824649]
is_a: ??:xxxx ! synonym

[Term]
id:
name: gene name
def: "The name of a gene." [PMID:31824649]
synonym: "gene" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! synonym

[Term]
id:
name: gene name synonym
def: "Synonymous name for a gene." [PMID:31824649]
is_a: ??:xxxx ! synonym

[Term]
id:
name: gene ontology synonym
def: "Synonym as used in Gene Ontology." [PMID:31824649]
synonym: "go synonym" EXACT PSI-ID-short []
is_a: ??:xxxx ! synonym

[Term]
id:
name: isoform synonym
def: "Synonymous name for an isoform." [PMID:31824649]
is_a: ??:xxxx ! synonym

<!-- ATTRIBUTE NAME - ROOT TERM FOR ATTRIBUTE ELEMENT ANNOTATION - name and nameAc attributes of idf:attribute elements to annotate free text stored as value of idf:attribute elements -->
<!-- in PSI-MI CV there is an additional level of terms between 'attribute name' and the terms actually used as descriptor, to specify to which element an attribute can be associated, e.g. feature attribute name, experiment attribute name, ... -->
<!-- these intermediate level terms are currently not present (except for bibliographic attribute name) in the CV version adopted for IDP, but can be easily inserted if necessary or desired-->

[Term]
id:
name: attribute name
def: "Collection of topics describing the free text stored as an attribute value." [PMID:31824649]
relationship: part_of ID:0000 ! intrinsically disordered protein

[Term]
id:
name: comment
def: "Comment for public view." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: url
def: "URL/Web address describing an object or entity." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: caution
def: "Warning about errors or grounds for confusion." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: experiment description
def: "The experimental text description may include information about host organisms, experimental methods and experimental conditions." [PMID:31824649]
synonym: "exp-description" EXACT PSI-ID-short []
is_a: ??:xxxx ! attribute name

[Term]
id:
name: experiment modification
def: "Modifications of the standard experimental method described in the CV." [PMID:31824649]
synonym: "exp-modification" EXACT PSI-ID-short []
is_a: ??:xxxx ! attribute name

[Term]
id:
name: experimental form description
def: "Free text description of all the modifications undergone by a molecule in the context of an an experiment." [PMID:31824649]
synonym: "experimental form" EXACT PSI-ID-short []
is_a: ??:xxxx ! attribute name

[Term]
id:
name: data-processing
def: "Comments on how the data was processed." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: isoform-comment
def: "Comments on the isoform of a molecule." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: antibodies
def: "This annotation topic should contain information about antibodies when specific antibodies (monoclonal or polyclonal raised against specific regions of the proteins or purified in a specific manner) have been used." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: library-used
def: "This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: feature description
def: "The feature text description may include information about the feature detection method." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: figure legend
def: "Text pointing to a specific paper figure legend where the experimental evidence for a structure state are to be found." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: function
def: "Biological function of a molecule or of a molecule region." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: search-url
def: "Search engine URL associated to CV database terms." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: disease
def: "A known or demonstrated disease association of a molecule or of a molecule region." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: pathway
def: "A metabolic or signalling pathway in which a molecule or a molecule region is involved." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: 3d-structure
def: "Comments on the 3D structure." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: 3d-work-r-factor
def: "Working R-Factor for the quality of the crystallographic model." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: 3d-free-r-factor
def: "Free R-Factor for the quality of the crystallographic model." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: 3d-resolution
def: "Resolution of the 3D structure." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: checksum
def: "A fixed-size datum calculated (by using a hash function) for a molecular sequence or structure, typically for purposes of error detection or indexing." [PMID:31824649]
synonym: "hashsum" RELATED []
is_a: ??:xxxx ! attribute name

[Term]
id:
name: resulting sequence
def: "Used to specify the identity of the residue (or residues) introduced by mutation or variant (of child terms). The attribute would be used concurrently with the description provided in the feature name." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: genomic coordinates
def: "Coordinates of a reference DNA sequence in the genome, providing information about the chromosome name, start and end of the sequence, optionally including the strand as well if it applies." [PMID:31824649]
synonym: "genomic coord" EXACT PSI-ID-short []
is_a: ??:xxxx ! attribute name

[Term]
id:
name: author-confidence
def: "Confidence classification assigned by the author of the publication to a specific structure state." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: confidence-mapping
def: "Description of confidence assessment for an experiment or structure state." [PMID:31824649]
is_a: ??:xxxx ! attribute name

[Term]
id:
name: validation regular expression
def: "Regular Expression used to check the validity of a cross-reference's identifier, generally associated to terms in CV Database." [PMID:31824649]
synonym: "id-validation-regexp" EXACT PSI-ID-short []
is_a: ??:xxxx ! attribute name

[Term]
id:
name: author submitted
def: "Data directly submitted by the authors to a database prior to publication." [PMID:31824649]
is_a: ??:xxxx ! attribute name

# bibliographic attribute names - to annotate attribute values related to a publication -->

[Term]
id:
name: bibliographic attribute name
def: "Attributes to specifically annotate a publication." [PMID:31824649]
synonym: "bib attribute" EXACT PSI-ID-short []
synonym: "publication attribute" EXACT []
is_a: ??:xxxx ! attribute name

[Term]
id:
name: contact-email
def: "E-mail address to contact the author or organisation which has produced the data." [PMID:31824649]
is_a: ??:xxxx ! bibliographic attribute name

[Term]
id:
name: contact-comment
def: "Free text notes on how to contact the author or organisation which has produced the data." [PMID:31824649]
is_a: ??:xxxx ! bibliographic attribute name

[Term]
id:
name: author-list
def: "List of authors associated to a publication." [PMID:31824649]
is_a: ??:xxxx ! bibliographic attribute name

[Term]
id:
name: curation request
def: "Annotation of a published paper which has been externally requested." [PMID:31824649]
is_a: ??:xxxx ! bibliographic attribute name

[Term]
id:
name: dataset
def: "Targeted curation dataset grouping experiments by topic or dataset origin." [PMID:31824649]
is_a: ??:xxxx ! bibliographic attribute name

[Term]
id:
name: journal
def: "Name and details of a journal from which a paper has been taken." [PMID:31824649]
is_a: ??:xxxx ! bibliographic attribute name

[Term]
id:
name: publication year
def: "Year of publication of a paper." [PMID:31824649]
is_a: ??:xxxx ! bibliographic attribute name

[Term]
id:
name: publication title
def: "Title of the publication." [PMID:31824649]
synonym: "title" EXACT PSI-ID-short []
is_a: ??:xxxx ! bibliographic attribute name

<!-- BIOLOGICAL ROLE - Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment. -->
<!-- currently we don't use/need this branch -->

<!-- CAUSAL INTERACTION - Binary causative relationships between biological entities. CV terms belonging to this term allow the description of causal interactions using the current PSI-MI schema. -->
<!-- currently we don't use/need this branch -->

<!-- COOPERATIVE INTERACTION - A set of molecular binding events that influence each other either positively or negatively through allostery or pre-assembly. In this context, covalent post-translational modifications are considered as binding events. CV terms that are part of this term allow the description of cooperative interactions using the current PSI-MI schema. -->
<!-- currently we don't use/need this branch -->

<!-- CROSS-REFERENCE TYPE - ROOT TERM FOR XREF ELEMENT ANNOTATION - refType and refTypeAc attributes of idf:dbReference elements to describe the type of information a cross-reference is pointing to -->

[Term]
id:
name: cross-reference type
def: "Qualifier to describe the type of information a cross-reference is pointing to." [PMID:31824649]
synonym: "refType" EXACT PSI-ID-alternate []
synonym: "xref type" EXACT PSI-ID-short []
relationship: part_of ID:0000 ! intrinsically disordered protein

[Term]
id:
name: gene product
def: "Reference of a protein object pointing to its genomic or nucleic acid sequence." [PMID:31824649]
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: isoform parent sequence reference
def: "Reference to the master sequence from which an isoform has been derived." [PMID:31824649]
synonym: "isoform-parent" EXACT PSI-ID-short []
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: cellular component
def: "Cross-reference pointing to a Gene Ontology - 'cellular component' term." [PMID:14681407]
synonym: "component" EXACT PSI-ID-short []
synonym: "go component term" EXACT PSI-ID-alternate []
xref: search-url: "https://www.ebi.ac.uk/QuickGO/term/${ac}"
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: molecular function
def: "Cross-reference pointing to a Gene Ontology - 'molecular function' term." [PMID:14681407]
synonym: "function" EXACT PSI-ID-short []
synonym: "go function term" EXACT PSI-ID-alternate []
xref: search-url: "https://www.ebi.ac.uk/QuickGO/term/${ac}"
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: biological process
def: "Cross reference pointing to a Gene Ontology - 'cellular process' term." [PMID:14681407]
synonym: "go process term" EXACT PSI-ID-alternate []
synonym: "process" EXACT PSI-ID-short []
xref: search-url: "https://www.ebi.ac.uk/QuickGO/term/${ac}"
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: identical object in an external resource
def: "Reference to the corresponding object in another database. Correspondence may be complete or partial." [PMID:31824649]
comment: For instance this qualifier, in an IDP structure state entry, can be associated to a cross reference to an experimentally determined structure of the same IDP region in another database.
synonym: "identity" EXACT PSI-ID-short []
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: partial identity match
def: "Reference to the corresponding object in another database. Correspondence is partial, so the objects are similar but explicitly not identical." [PMID:31824649]
synonym: "partial match" EXACT PSI-ID-short []
synonym: "similar object in an external resource" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: primary-reference
def: "Used to indicate the PMID from which the experimental data is extracted." [PMID:31824649]
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: secondary accession number
def: "Reference to the corresponding object in another database, but the identifier used in the external database is a secondary identifier or former accession number." [PMID:31824649]
synonym: "secondary-ac" EXACT PSI-ID-short []
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: multiple parent reference
def: "Qualifier used for hybrid or composite molecules with more than one cross-reference to parent molecules." [PMID:31824649]
subset: PSI-MI_slim
synonym: "multiple parent" EXACT PSI-MI-short []
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: inferred-from
def: "Refers to the original experimentally verified object from which the described object has been derived." [PMID:25313161]
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: subset
def: "Reference to the corresponding object in another database, implying the object is part of a cross-referenced entity (usually a complex)." [PMID:31824649]
synonym: "part of" EXACT PSI-ID-alternate []
synonym: "subset" EXACT PSI-ID-short []
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: method reference
def: "Reference to a related paper which more fully describes either the experimental method or one or more of the molecules used within the experiment." [PMID:31824649]
is_a: ??:xxxx ! cross-reference type

[Term]
id:
name: additional information
def: "Related object within the same database or pointing to an external database." [PMID:31824649]
synonym: "see-also" EXACT PSI-ID-short []
is_a: ??:xxxx ! cross-reference type

<!-- CURATION CONTENT - Indicates source, depth and standards by which an entry has been added to a database. -->
<!-- currently we don't use/need this branch -->

<!-- CURATION QUALITY - An assessment of the depth and extent to which a paper has been curated -->
<!-- currently we don't use/need this branch -->

<!-- DATABASE CITATION - ROOT TERM FOR DATABASE REFERENCING (XREF ELEMENT) - db and dbAc attributes of idf:dbReference elements to define external resources -->

[Term]
id:
name: database citation
def: "Database citation lists names of databases commonly used to cross reference IDP data." [PMID:31824649]
relationship: part_of ID:0000 ! intrinsically disordered protein

[Term]
id:
name: psi-mi
def: "PSI-MI." [PMID:14755292]
synonym: "PSI-MI" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "MI:[0-9]{4}"
xref: search-url: "http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=${ac}"
is_a: ??:xxxx ! database citation

# NEW TERM
[Term]
id:
name: psi-id
def: "PSI-ID." [PMID:31824649]
synonym: "PSI-ID" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "ID:[0-9]{4}"
xref: search-url: "http://www.ebi.ac.uk/ols/ontologies/id/terms?obo_id=${ac}"
is_a: ??:xxxx ! database citation

# NEW TERM
[Term]
id:
name: idpo
def: "The IDPontology is organized in five different branches/aspects ("namespace" in the DisProt and OBO formats) and is maintained by DisProt consortium." [PMID:27899601]
synonym: "IDPO" EXACT PSI-ID-alternate []
xref: search-url: "https://www.disprot.org/about"
is_a: ??:xxxx ! database citation

# experiment database

[Term]
id:
name: experiment database
def: "Database that contains information used to add additional information to experiments (meta-data)." [PMID:31824649]
synonym: "experiment xref" EXACT PSI-ID-short []
is_a: ??:xxxx ! database citation

[Term]
id:
name: evidence and conclusion ontology
def: "The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means." [PMID:30407590]
synonym: "ECO" EXACT PSI-ID-short []
xref: id-validation-regexp: "ECO:\\d{7}$"
xref: search-url: "http://www.ebi.ac.uk/ols/ontologies/ECO/terms?obo_id=${ac}"
is_a: ??:xxxx ! experiment database

[Term]
id:
name: experimental factor ontology
def: "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables, combining parts of several biological ontologies to additional new terms." [pmid:20200009]
synonym: "EFO" EXACT PSI-ID-short []
xref: id-validation-regexp: "\\d{7}$"
xref: search-url: "http://www.ebi.ac.uk/ols/ontologies/efo/terms?obo_id=${ac}"
is_a: ??:xxxx ! experiment database

[Term]
id:
name: edam
def: "EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats.\nhttp://edamontology.org/" [PMID:23479348]
synonym: "EDAM" EXACT PSI-ID-alternate []
synonym: "EMBRACE Data And Methods" EXACT PSI-ID-alternate []
xref: url:http\://edamontology.org/
is_a: ??:xxxx ! experiment database

# feature database

[Term]
id:
name: feature database
def: "A database describing a feature on a molecule." [PMID:31824649]
synonym: "feature xref" EXACT PSI-ID-short []
is_a: ??:xxxx ! database citation

[Term]
id:
name: gene ontology
def: "The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products.\nhttp://www.ebi.ac.uk/GO" [PMID:30395331]
synonym: "go" EXACT PSI-ID-short []
xref: id-validation-regexp: "GO:[0-9]{7}"
xref: search-url: "https://www.ebi.ac.uk/QuickGO/term/${ac}"
is_a: ??:xxxx ! feature database
is_a: ??:xxxx ! interaction database

[Term]
id:
name: go_central
def: "The GO Consortium coordinated an effort to maximize and optimize GO annotations for a large and representative set of key genomes, known as 'reference genomes'. The Reference Genome Annotation Project aimed to completely annotate twelve reference genomes, producing a resource that may effectively seed automatic annotation efforts of other genomes. This resource represents manual annotation from PAINT curators into the UniProt Protein2GO curation tool.\nhttp://www.geneontology.org/GO.refgenome.shtml" [PMID:19578431]
synonym: "GO central" EXACT PSI-ID-alternate []
synonym: "go_central" EXACT PSI-ID-short []
synonym: "GO_central" EXACT PSI-ID-alternate []
synonym: "The Reference Genome Annotation Project" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! gene ontology

[Term]
id:
name: cdd
def: "The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence.\nhttp://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml" [PMID:14755292]
synonym: "CDD" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[0-9]+"
is_a: ??:xxxx ! feature database

[Term]
id:
name: interpro
def: "InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences.\nhttps://www.ebi.ac.uk/interpro/" [PMID:30398656]
synonym: "InterPro" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "IPR[0-9]{6}"
xref: search-url: "https://www.ebi.ac.uk/interpro/entry/InterPro/${ac}"
is_a: ??:xxxx ! feature database

[Term]
id:
name: gene3d
def: "The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species.\nhttp://cathwww.biochem.ucl.ac.uk:8080/Gene3D/" [PMID:29112716]
synonym: "Gene3D" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! interpro

[Term]
id:
name: pirsf
def: "PIRSF is a classification system based on evolutionary relationship of whole proteins.\nhttp://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml" [PMID:14681371]
synonym: "PIRSF" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "PIRSF[0-9]{5}"
is_a: ??:xxxx ! interpro

[Term]
id:
name: prints
def: "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family.\nhttp://umber.sbs.man.ac.uk/dbbrowser/PRINTS/" [PMID:7971946]
synonym: "PRINTS" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "PR[0-9]{6}"
is_a: ??:xxxx ! interpro

[Term]
id:
name: prodom
def: "The ProDom protein domain database consists of an automatic compilation of homologous domains.\nhttp://protein.toulouse.inra.fr/prodom.html" [PMID:9399865]
synonym: "ProDom" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "PD[0-9]{6}"
is_a: ??:xxxx ! interpro

[Term]
id:
name: tigrfams
def: "TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation.\nhttp://www.tigr.org/TIGRFAMs" [PMID:23197656]
synonym: "TIGRFAMs" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "TIGR[0-9]+"
is_a: ??:xxxx ! interpro

[Term]
id:
name: panther
def: "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.\nwww.pantherdb.org/" [PMID:30407594]
synonym: "PANTHER" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! interpro

[Term]
id:
name: pfam
def: "Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.\nhttp://www.sanger.ac.uk/Software/Pfam" [PMID:30357350 ]
synonym: "Pfam" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "PF[0-9]{5}"
is_a: ??:xxxx ! interpro

[Term]
id:
name: prosite
def: "PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles.\nhttp://us.expasy.org/prosite/" [PMID:16381852]
synonym: "Prosite" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "PS[0-9]{5}"
is_a: ??:xxxx ! interpro

[Term]
id:
name: scop superfamily
def: "SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain.\nhttp://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/" [PMID:31724711]
synonym: "SCOP superfamily" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[0-9]+"
is_a: ??:xxxx ! interpro

[Term]
id:
name: smart
def: "SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures.\nhttp://smart.embl-heidelberg.de/" [PMID:9600884]
synonym: "SMART" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "SM[0-9]{5}"
is_a: ??:xxxx ! interpro

[Term]
id:
name: eukaryotic linear motif resource
def: "The ELM resource provides a database of curated short linear motif classes and instances, as well as a sequence analysis tool to detect putative short linear motif instances in query sequences. http://elm.eu.org/" [PMID:22110040]
synonym: "elm" EXACT PSI-ID-short []
xref: id-validation-regexp: "[A-Za-z_0-9]+$"
xref: search-url: "http://elm.eu.org/elms/elmPages/${ac}.html"
is_a: ??:xxxx ! feature database

[Term]
id:
name: ipfam
def: "Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at.\nhttp://www.sanger.ac.uk/Software/Pfam/iPfam/" [PMID:15353450]
is_a: ??:xxxx ! feature database

[Term]
id:
name: cog
def: "Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain." [PMID:11125040]
synonym: "Clusters of Orthologous Groups" EXACT []
synonym: "cogg" EXACT PSI-ID-short []
is_a: ??:xxxx ! feature database

[Term]
id:
name: wwpdb
def: "The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.\nhttp://www.wwpdb.org/" [PMID:14634627]
synonym: "wwPDB" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[0-9][a-zA-Z0-9]{3}"
xref: search-url: "http://www.pdbe.org/${ac}"
is_a: ??:xxxx ! feature database
is_a: ??:xxxx ! interaction database
is_a: ??:xxxx ! source database

[Term]
id:
name: pdbe
def: "The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB).\nhttp://www.ebi.ac.uk/pdbe/" [PMID:16381867]
synonym: "e-MSD" EXACT []
synonym: "MSD" RELATED []
synonym: "PQS" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[0-9][a-zA-Z0-9]{3}"
xref: search-url: "http://www.ebi.ac.uk/pdbe/entry/pdb/${ac}"
is_a: ??:xxxx ! wwpdb

[Term]
id:
name: emdb
def: "The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files." [PMID:14643225]
synonym: "Electron Microscopy Data Bank" EXACT PSI-ID-alternate []
synonym: "eMDB" EXACT PSI-ID-short []
xref: search-url: "https://www.ebi.ac.uk/pdbe/entry/emdb/${ac}"
is_a: ??:xxxx ! pdbe

[Term]
id:
name: empiar
def: "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. The purpose of EMPIAR is to provide easy access to state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D volumes are stored, and uses the fault-tolerant Aspera platform for data transfers.\n\nhttps://www.ebi.ac.uk/pdbe/emdb/empiar/" [PMID:27067018]
synonym: "Electron Microscopy Public Image Archive" EXACT PSI-ID-alternate []
synonym: "EMPIAR" EXACT PSI-ID-alternate []
synonym: "empiar" EXACT PSI-ID-short []
xref: id-validation-regex: "EMPIAR-[0-9]{5}"
xref: search-url: "https://dx.doi.org/10.6019/${ac}"
is_a: ??:xxxx ! emdb

[Term]
id:
name: pdbj
def: "PDBj (Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites.\nhttp://www.pdbj.org/" [PMID:12099029]
synonym: "PDBj" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[0-9][a-zA-Z0-9]{3}"
xref: search-url: "http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/DetailServlet?PDBID=${ac}&PAGEID=Summary"
is_a: ??:xxxx ! wwpdb

[Term]
id:
name: rcsb pdb
def: "The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. \nhttp://www.pdb.org/" [PMID:14634627]
synonym: "PDB" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[0-9][a-zA-Z0-9]{3}"
xref: search-url: "http://www.pdb.org/pdb/explore/explore.do?structureId=${ac}"
is_a: ??:xxxx ! wwpdb

[Term]
id:
name: heterogen
def: "The HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for\nwhich coordinates are supplied. Groups are considered HET if they are: \n- not one of the standard amino acids, and \n- not one of the nucleic acids (C, G, A, T, U, and I), and \n- not one of the modified versions of nucleic acids (+C, +G, +A,\n+T, +U, and +I), and \n- not an unknown amino acid or nucleic acid where UNK is used to\nindicate the unknown residue name. \nHet records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNK." [PMID:31824649]
synonym: "het" EXACT PSI-ID-short []
is_a: ??:xxxx ! rcsb pdb
is_a: ??:xxxx ! pdbe
is_a: ??:xxxx ! pdbj

## feature db, PTM

[Term]
id:
name: protein modification ontology
def: "Catalogue of covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue." [PMID:18688235]
synonym: "psi-mod" EXACT PSI-ID-short []
xref: id-validation-regexp: "MOD:[0-9]{5}"
is_a: ??:xxxx ! feature database

[Term]
id:
name: resid
def: "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.\nhttp://www.ebi.ac.uk/RESID/index.html" [PMID:15174122]
xref: id-validation-regexp: "AA[0-9]{4}"
xref: search-url: "http://srs.ebi.ac.uk/cgi-bin/wgetz?[resid-id:${ac}]+-e"
is_a: ??:xxxx ! feature database

[Term]
id:
name: deltamass
def: "A database of protein post translational modifications. www.abrf.org/index.cfm/dm.home" [PMID:8322616]
is_a: ??:xxxx ! feature database

[Term]
id:
name: unimod
def: "A database of protein modifications for mass spectrometry. www.unimod.org" [PMID:15174123]
is_a: ??:xxxx ! feature database

## feature db, variants

[Term]
id:
name: dbsnp
def: "dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations." [PMID:11125122]
synonym: "dbSNP" EXACT PSI-ID-alternate []
synonym: "dbsnp" EXACT PSI-ID-short []
xref: search-url: "https://www.ncbi.nlm.nih.gov/snp/${ac}"
is_a: ??:xxxx ! feature database

[Term]
id:
name: clinvar
def: "ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. \nhttps://www.ncbi.nlm.nih.gov/clinvar" [PMID:29165669]
synonym: "ClinVAR" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[0-9]+"
xref: search-url: "https://www.ncbi.nlm.nih.gov/clinvar/variation/${ac}"
is_a: ??:xxxx ! feature database

# new terms for database citation related to IDP (feature or source db's ?)

# NEW TERM
[Term]
id:
name: idpcentral / disprotcentral ?
def: "An umbrella consortium for central management of protein disorder related tools and databases." [PMID:22453911]
subset: PSI-MI_slim
synonym: "IDPcentral" EXACT PSI-ID-alternate []
xref: search-url: "http://www.ebi.ac.uk/intact/imex/main.xhtml?query=${ac}"
is_a: ??:xxxx ! feature database ? or source database ?
? add as parent term to db's integrated in disprot central ?

# NEW TERM
[Term]
id:
name: disprot
def: "DisProt is a database of manually curated annotations of experimental disorder, collected from the literature.\nhttps://www.disprot.org/" [PMID:27899601]
synonym: "DisProt" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! feature database ? maybe also source database?

# NEW TERM
[Term]
id:
name: bmrb
def: "The Biological Magnetic Resonance Data Bank (BMRB) is a repository for data from NMR spectroscopy on proteins, peptides, nucleic acids, and other biomolecules.\nhttps://bmrb.io/" [PMID:32006287]
synonym: "BMRB" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! feature database or is_a: ??:xxxx ! wwpdb ? maybe also source database?

# a term for BMRB already exists in PSI-MI CV, however, defined as an interaction database
[Term]
id:
name: bmrb
def: "Database for NMR spectroscopy information on biomolecules hosted at the University of Wisconsin, Madison, US." [PMID:18288446]
synonym: "Biological Magnetic Resonance Data Bank" RELATED []
synonym: "BioMagResBank" RELATED []
is_a: ??:xxxx ! interaction database

# NEW TERM
[Term]
id:
name: sasbdb
def: "The Small Angle Scattering Biological Data Bank (SASBDB) is a fully searchable curated repository of freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.\nhttps://www.sasbdb.org/" [PMID:31576635]
synonym: "SASBDB" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! feature database ? maybe also source database?

# NEW TERM
[Term]
id:
name: pcddb
def: "The Protein Circular Dichroism Data Bank (PCDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data and their associated experimental metadata.\nhttps://pcddb.cryst.bbk.ac.uk/" [PMID:21071417]
synonym: "PCDDB" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! feature database ? maybe also source database?

# NEW TERM
[Term]
id:
name: dibs
def: "Disordered Binding Site (DIBS) database is a repository for protein complexes that are formed between Intrinsically Disordered Proteins (IDPs) and globular/ordered partner proteins.\nhttp://dibs.enzim.ttk.mta.hu/" [PMID:29385418]
synonym: "DIBS" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! feature database ? maybe also source database?
is_a: ??:xxxx ! interaction database

# NEW TERM
[Term]
id:
name: mobidb
def: "MobiDB provides information about intrinsically disordered regions (IDRs) and related features from various sources and prediction tools. Different levels of reliability and different features are reported as different and independent annotations.\nhttps://mobidb.bio.unipd.it/" [PMID:33237329]
synonym: "MobiDB" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! feature database ? maybe also source database?

# NEW TERM
[Term]
id:
name: mfib
def: "Mutual Folding Induced by Binding (MFIB) database is a repository for protein complexes that are formed exclusively by intrinsically unstructured proteins (IUPs).\nhttp://mfib.enzim.ttk.mta.hu/" [PMID:29036655]
synonym: "MFIB" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! feature database ? maybe also source database?
is_a: ??:xxxx ! interaction database

# NEW TERM
[Term]
id:
name: ideal
def: "Intrinsically Disordered proteins with Extensive Annotations and Literature (IDEAL) provides a collection of knowledge on experimentally verified intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and posttranslational modification sites together with references and structural domain assignments.\nhttps://www.ideal-db.org/" [PMID:22067451]
synonym: "IDEAL" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! feature database ? maybe also source database?

# NEW TERM
[Term]
id:
name: ped
def: "The Protein Ensemble Database (PED) is an open access database for the deposition of structural ensembles, mainly intrinsically disordered proteins (IDPs), measured with nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, and fluorescence resonance energy transfer.\nhttps://proteinensemble.org/" [PMID:33305318]
synonym: "PED" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! feature database ? maybe also source database?

# interaction (& pathway) database: can we use MI terms/id's for this, as they are defined there?

# literature database

[Term]
id:
name: literature database
def: "Database acting as a source of literature information." [PMID:31824649]
synonym: "literature xref" EXACT PSI-ID-short []
synonym: "publication xref" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! database citation

[Term]
id:
name: pubmed
def: "PubMed is designed to provide access to citations from biomedical literature. The data can be found at both NCBI PubMed and Europe PubMed Central. \nhttp://www.ncbi.nlm.nih.gov/pubmed\nhttp://europepmc.org" [PMID:31824649]
xref: id-validation-regexp: "[0-9]+"
xref: search-url: "http://europepmc.org/abstract/MED/${ac}"
is_a: ??:xxxx ! literature database

[Term]
id:
name: pubmed central
def: "PubMed Central is the US National Institute of Health free digital archive of biomedical and life science journals." [PMID:12519941]
synonym: "pmc" EXACT PSI-ID-short []
is_a: ??:xxxx ! literature database

[Term]
id:
name: digital object identifier
def: "Identifier of a publication prior to pubmed indexing." [PMID:31824649]
synonym: "doi" EXACT PSI-ID-short []
xref: id-validation-regexp: "\\d+.\\d+/[a-zA-Z0-9\\.\\:]+"
xref: search-url: "http://dx.doi.org/${ac}"
is_a: ??:xxxx ! literature database

[Term]
id:
name: biorxiv
def: "bioRxiv is a free online archive and distribution service for unpublished preprints in the life sciences, operated by Cold Spring Harbor Laboratory. Articles are not peer-reviewed, edited, or typeset before being posted online.\nhttp://biorxiv.org/" [PMID:]
synonym: "bioRxiv" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "\\d+.\\d+/[a-zA-Z0-9\\.\\:]+"
xref: search-url: "https://www.biorxiv.org/content/${ac}"
is_a: ??:xxxx ! literature database

# participant database --> this needs to be adopted to IDP standard, region database, or molecule database, or experimental construct database ?

[Term]
id:
name: region database or molecule database or experimental construct database ?
def: "Database for cross-referencing molecules or regions thereof analysed in experiments." [PMID:31824649]
synonym: "region xref" or "molecule xref" or "experimental construct xref" EXACT PSI-ID-short [] ?
is_a: ??:xxxx ! database citation

## participant/sequence db

[Term]
id:
name: sequence database
def: "Database collecting nucleic or amino acid sequences mainly derived from genomic or mRNA sequencing." [PMID:31824649]
is_a: ??:xxxx ! region database or molecule database or experimental construct database ?

[Term]
id:
name: sequence ontology
def: "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data." [PMID:15892872]
synonym: "so" EXACT PSI-ID-short []
xref: id-validation-regexp: "SO:[0-9]{7}"
is_a: ??:xxxx ! feature database
is_a: ??:xxxx ! participant database

## participant/sequence db, peptide

[Term]
id:
name: peptide sequence database
def: "database storing sequences detected by peptide identification methods." [PMID:31824649]
synonym: "pep seq db" EXACT PSI-ID-short []
is_a: ??:xxxx ! sequence database

[Term]
id:
name: pride
def: "PRIDE is a public repository of protein and peptide identifications for the proteomics community.\nhttp://www.ebi.ac.uk/pride/" [PMID:16381953]
xref: search-url: "http://www.ebi.ac.uk/pride/archive/projects/${ac}"
is_a: ??:xxxx ! peptide sequence database

[Term]
id:
name: peptide atlas
def: "PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms.\nhttp://www.peptideatlas.org/" [PMID:16381952]
synonym: "PeptideAtlas" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! peptide sequence database

[Term]
id:
name: gpm
def: "Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results.\nhttp://www.thegpm.org" [PMID:15595733]
synonym: "Global Proteome Machine" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! peptide sequence database

[Term]
id:
name: proteomexchange
def: "The ProteomeXchange consortium was set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. The data is actually hosted by consortium member databases like PeptideAtlas or PRIDE. \n\nhttp://www.proteomexchange.org" [PMID:25047258]
synonym: "proteomexchange" EXACT PSI-ID-short []
synonym: "ProteomExchange" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! peptide sequence database

## participant/sequence db, protein

[Term]
id:
name: protein sequence database
def: "Database dedicated to the collection and annotation of protein sequences." [PMID:21447597]
synonym: "protein seq db" EXACT PSI-ID-short []
is_a: ??:xxxx ! sequence database

[Term]
id:
name: uniprot
def: "UniProt is a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, interpreting, integrating and standardizing data from numerous sources and is the most comprehensive catalog of protein sequences and functional annotation." [PMID:21051339]
synonym: "uniprot" EXACT PSI-ID-short []
is_a: ??:xxxx ! protein sequence database

[Term]
id:
name: uniparc
def: "UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources.\nhttp://www.ebi.ac.uk/uniparc/" [PMID:14681372]
synonym: "UniParc" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "UPI[A-F0-9]{10}"
xref: search-url: "http://www.ebi.uniprot.org/entry/${ac}"
is_a: ??:xxxx ! uniprot

[Term]
id:
name: uniprot knowledge base
def: "UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.\nhttp://www.uniprot.org" [PMID:14681372]
synonym: "uniprotkb" EXACT PSI-ID-short []
synonym: "UniProtKB" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}-PRO_[0-9]{10}"
xref: search-url: "http://www.uniprot.org/uniprot/${ac}"
is_a: ??:xxxx ! interaction database
is_a: ??:xxxx ! uniprot

[Term]
id:
name: uniprot/swiss-prot
def: "UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProtKB/Swiss-Prot is manually curated which means that the information in each entry is annotated and reviewed by a curator. \nhttp://www.uniprot.org" [PMID:14681372, PMID:21447597]
synonym: "swiss-prot" EXACT PSI-ID-short []
synonym: "UniProt" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}-PRO_[0-9]{10}"
xref: search-url: "http://www.uniprot.org/uniprot/${ac}"
is_a: ??:xxxx ! uniprot knowledge base

[Term]
id:
name: uniprot/trembl
def: "UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. The records in UniProtKB/TrEMBL are automatically generated and are enriched with automatic annotation and classification.\nhttp://www.uniprot.org" [PMID:14681372, PMID:21447597]
synonym: "trembl" EXACT PSI-ID-short []
synonym: "UniProt" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}-PRO_[0-9]{10}"
xref: search-url: "http://www.uniprot.org/uniprot/${ac}"
is_a: ??:xxxx ! uniprot knowledge base

[Term]
id:
name: refseq
def: "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms.\nhttp://www.ncbi.nlm.nih.gov/RefSeq/" [PMID:26553804]
synonym: "Refseq" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[XNZ][A-Z]_[0-9]+|[0-9]+|[XNZ][A-Z]_[0-9]+\\.[0-9]+"
is_a: ??:xxxx ! protein sequence database

[Term]
id:
name: human orfeome collection
def: "A central resource of single-colony, fully-sequenced cloned human ORFs which can be readily transferred to Gateway compatible destination vectors for various functional proteomics studies. This set of ORFs ranges in size from 75 to more than 10,000 base pairs, and contains over 1,000 ORFs from genes with multiple splice variants." [PMID:15489335]
xref: search-url: "http://horfdb.dfci.harvard.edu/"
is_a: ??:xxxx ! protein sequence database

[Term]
id:
name: pir
def: "The PIR-International Protein Sequence Database (PIR-PSD) was the world's first database of classified and functionally annotated protein sequences that grew out of the Atlas of Protein Sequence and Structure (1965-1978) edited by Margaret Dayhoff. Produced and distributed by the Protein Information Resource in collaboration with MIPS (Munich Information Center for Protein Sequences) and JIPID (Japan International Protein Information Database), PIR-PSD has been the most comprehensive and expertly-curated protein sequence database in the public domain for over 20 years. In 2002, PIR joined EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics) to form the UniProt consortium. PIR-PSD sequences and annotations have been integrated into UniProt Knowledgebase. Bi-directional cross-references between UniProt (UniProt Knowledgebase and/or UniParc) and PIR-PSD are established to allow easy tracking of former PIR-PSD entries. PIR-PSD unique sequences, reference citations, and experimentally-verified data can now be found in the relevant UniProt records. \n\nLegacy data can be found at \nhttp://pir.georgetown.edu/pirwww/dbinfo/pir_psd.shtml" [PMID:10592177]
synonym: "PIR" EXACT PSI-ID-alternate []
synonym: "Protein Information Resource" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! protein sequence database

[Term]
id:
name: international protein index
def: "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources." [PMID:15221759]
synonym: "ipi" EXACT PSI-ID-short []
xref: id-validation-regexp: "IPI[0-9]+.[0-9]+|IPI[0-9]+"
is_a: ??:xxxx ! protein sequence database

## participant/sequence db, rna

[Term]
id:
name: rfam
def: "Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families.\nhttp://www.sanger.ac.uk/Software/Rfam/" [PMID:29112718]
synonym: "rfam" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "RF[0-9]{5}"
is_a: ??:xxxx ! sequence database

[Term]
id:
name: RNAcentral
def: "Provides unified access to the ncRNA sequence data supplied by the expert databases." [PMID:25352543]
xref: id-validation-regexp: "/URS[0-9A-F]{10}/i"
xref: search-url: "http://rnacentral.org/rna/${ac}"
is_a: ??:xxxx ! sequence database

## participant/sequence db, genome

[Term]
id:
name: genome database
def: "Database responsible for the maintenance and subsequent annotation of one or more genomic sequences." [PMID:31824649]
synonym: "genome db" EXACT PSI-ID-short []
is_a: ??:xxxx ! sequence database

[Term]
id:
name: cygd
def: "The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.\nhttp://mips.gsf.de/proj/yeast/CYGD.\nhttp://mips.gsf.de/genre/proj/mpact" [PMID:]
synonym: "CYGD" EXACT PSI-ID-alternate []
synonym: "CYGD (MIPS)" EXACT PSI-ID-alternate []
synonym: "MIPS" EXACT PSI-ID-alternate []
synonym: "MPact" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[0-9]+|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|[A-Z0-9]+\\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9]"
is_a: ??:xxxx ! source database
is_a: ??:xxxx ! genome database
is_a: ??:xxxx ! pathways database

[Term]
id:
name: flybase
def: "FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila.\nhttp://flybase.org" [PMID:]
synonym: "FlyBase" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "FB[a-z]{2}[0-9]{7}"
xref: search-url: "http://flybase.org/reports/${ac}"
is_a: ??:xxxx ! genome database

[Term]
id:
name: mgd/mgi
def: "Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.\nhttp://www.informatics.jax.org/" [PMID:]
synonym: "MGD/MGI" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "MGI:[0-9]+"
is_a: ??:xxxx ! genome database

[Term]
id:
name: ensembl
def: "Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes.\nhttp://www.ensembl.org" [PMID:15078858]
synonym: "Ensembl" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "ENS[A-Z]+[0-9]{11}|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|CG[0-9]+|[A-Z0-9]+\\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9]"
xref: search-url: "http://www.ensembl.org/Multi/Search/Results?q=${ac}"
is_a: ??:xxxx ! genome database

[Term]
id:
name: rgd
def: "The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data.\nhttp://rgd.mcw.edu/" [PMID:]
synonym: "RGD" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[0-9]+"
is_a: ??:xxxx ! genome database

[Term]
id:
name: sgd
def: "SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.\nhttp://www.yeastgenome.org/" [PMID:]
synonym: "Saccharomyces Genome Database" EXACT PSI-ID-alternate []
synonym: "SGD" EXACT PSI-ID-short []
xref: id-validation-regexp: "S[0-9]{9}"
xref: search-url: "http://www.yeastgenome.org/locus/${ac}/overview"
is_a: ??:xxxx ! genome database

[Term]
id:
name: wormbase
def: "WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser.\nhttp://www.wormbase.org/" [PMID:]
subset: PSI-MI_slim
synonym: "WormBase" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "WBGene[0-9]{8}"
is_a: ??:xxxx ! genome database

[Term]
id:
name: encode
def: "ENCODE (the Encyclopedia Of DNA Elements) seeks to identify all protein-coding genes. The current ENCODE data set is derived from 1% of the human genome and has been selected for analysis in the pilot phase of the project.\nhttp://www.genome.gov/10005107" [PMID:17372197]
synonym: "ENCODE" EXACT PSI-ID-alternate []
synonym: "Encyclopedia Of DNA Elements" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! genome database

[Term]
id:
name: camjedb
def: "Camjedb is a comprehensive database for information on the genome of Campylobacter jejuni.\nhttp://www.sanger.ac.uk/Projects/C_jejuni/" [PMID:106882042]
is_a: ??:xxxx ! genome database

[Term]
id:
name: ensemblgenomes
def: "Genome browser complementary to Ensembl which extends the search space across a broader taxonomic range.\nhttp://www.ensemblgenomes.org" [PMID:19884133]
xref: search-url: "http://ensemblgenomes.org/search/eg/${ac}"
is_a: ??:xxxx ! genome database

[Term]
id:
name: dictybase
def: "dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome." []
xref: id-validation-regexp: "DDB_G(0-9){7}"
is_a: ??:xxxx ! genome database

[Term]
id:
name: rice genome annotation project
def: "NSF funded annotation project." [PMID:17145706]
synonym: "RGAP" RELATED []
is_a: ??:xxxx ! genome database

[Term]
id:
name: plantgdb
def: "PlantGDB develops plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities." [PMID:18063570]
synonym: "plantgdb" EXACT PSI-ID-short []
is_a: ??:xxxx ! genome database

[Term]
id:
name: ratmap
def: "The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB Genetics at Gothenburg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap." [PMID:15608244]
synonym: "ratmap" EXACT PSI-ID-short []
is_a: ??:xxxx ! genome database

[Term]
id:
name: tair
def: "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community." [PMID:20521243]
synonym: "tair" EXACT PSI-ID-short []
synonym: "The Arabidopsis Information Resource" EXACT []
is_a: ??:xxxx ! genome database

[Term]
id:
name: tigr/jcvi
def: "The J. Craig Venter Institute was formed in October 2006 through the merger of several affiliated and legacy organizations including The Institute for Genomic Research (TIGR)." [PMID:18287690]
synonym: "J. Craig Venter Institute" EXACT []
synonym: "The Institute for Genomic Research" EXACT PSI-ID-short []
synonym: "tigr/jcvi" EXACT PSI-ID-short []
is_a: ??:xxxx ! genome database

[Term]
id:
name: zfin
def: "Extensive information on Danio rerio, including genomics databases, developmental stages, publications and molecular tools." [PMID:21036866]
synonym: "The Zebrafish Model Organism Database " EXACT []
synonym: "zfin" EXACT PSI-ID-short []
is_a: ??:xxxx ! genome database

## participant db, gene

[Term]
id:
name: gene database
def: "Primarily nomenclature/cross-reference database, used by curators to establish a link between a gene and protein ID. In some cases, database records do not contain actual sequence but point to loci on specific reference genomes." [PMID:31824649]
synonym: "gene db" EXACT PSI-ID-short []
is_a: ??:xxxx ! region database or molecule database or experimental construct database ?

[Term]
id:
name: hgnc
def: "HGNC is the nomenclature committee responsible for the naming of human genes." [PMID:20929869]
synonym: "hgnc" EXACT PSI-MI-short []
synonym: "Human Genome Nomenclature Committee" EXACT PSI-ID-short []
is_a: ??:xxxx ! gene database

[Term]
id:
name: entrez gene/locuslink
def: "LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci.\nhttp://www.ncbi.nlm.nih.gov/LocusLink/" [PMID:]
synonym: "Entrez gene/locuslink" EXACT PSI-ID-alternate []
synonym: "entrezgene/locuslink" EXACT PSI-ID-short []
xref: id-validation-regexp: "[0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+"
is_a: ??:xxxx ! gene database

## participant/sequence db, genbank

[Term]
id:
name: ddbj/embl/genbank
def: "DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation.\nhttp://www.ebi.ac.uk/embl/Contact/collaboration" [PMID:29190397]
synonym: "DDBJ" EXACT PSI-ID-alternate []
synonym: "DDBJ/EMBL/GenBank" EXACT PSI-ID-alternate []
synonym: "EMBL" EXACT PSI-ID-alternate []
synonym: "GenBank" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[A-Z][0-9]{5}|[A-Z][0-9]{5}\\.[0-9]+|[A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\\.[0-9]+|[A-Z]{4}[0-9]{8}|[A-Z]{4}[0-9]{8}\\.[0-9]+"
xref: search-url: "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBLSVA&id=${ac}"
is_a: ??:xxxx ! sequence database

[Term]
id:
name: genbank identifier
def: "GenBank Identifier or GI numbers for nucleotides or proteins" [PMID:15078858]
xref: id-validation-regexp: "ENS[A-Z]+[0-9]{11}"
is_a: ??:xxxx ! sequence database

[Term]
id:
name: protein genbank identifier
def: "GenBank Identifier or GI numbers for proteins." [PMID:17170002]
synonym: "GenBank Protein GI" EXACT PSI-ID-alternate []
synonym: "genbank protein gi" EXACT PSI-ID-alternate []
synonym: "genbank_protein_gi" EXACT PSI-ID-short []
synonym: "genpept id" EXACT []
xref: id-validation-regexp: "[0-9]+"
xref: search-url: "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=Retrieve&dopt=Graphics&list_uids=${ac}"
is_a: ??:xxxx ! genbank identifier

[Term]
id:
name: nucleotide genbank identifier
def: "GenBank Identifier or GI numbers for nucleotide." [PMID:17170002]
synonym: "genbank nucleotide" EXACT PSI-ID-alternate []
synonym: "GenBank Nucleotide" EXACT PSI-ID-alternate []
synonym: "genbank_nucl_gi" EXACT PSI-ID-short []
xref: id-validation-regexp: "[0-9]+"
xref: search-url: "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=Retrieve&dopt=Graphics&list_uids=$"
is_a: ??:xxxx ! genbank identifier

## participant/sequence db, other

[Term]
id:
name: chembl target
def: "ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets." []
xref: regexp: "CHEMBL:[0-9]+"
xref: search-url: "http://www.ebi.ac.uk/chembldb/index.php/target/inspect/${ac}"
is_a: ??:xxxx ! sequence database
relationship: part_of ??:xxxx ! chembl

[Term]
id:
name: flannotator
def: "A repository for collecting, storing and and searching the annotation of gene or protein expression patterns in Drosophila melongaster. CPTI (Cambridge Protein Trap Identifier)" [PMID:19126575]
xref: id-validation-regexp: "CPTO-[0-9]{6}"
is_a: ??:xxxx ! sequence database

[Term]
id:
name: huge
def: "A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project.\nhttp://www.kazusa.or.jp/huge/" [PMID:]
xref: id-validation-regexp: "KIAA[0-9]{4}[A-Z]{0,1}"
xref: search-url: "http://www.kazusa.or.jp/huge/gfpage/${ac}"
is_a: ??:xxxx ! sequence database

[Term]
id:
name: omim
def: "Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases.\nhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM" [PMID:]
synonym: "OMIM" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[0-9]+"
xref: search-url: "http://www.omim.org/entry/${ac}"
is_a: ??:xxxx ! sequence database

## participant db, source organism

[Term]
id:
name: uniprot taxonomy
def: "Based on NCBO Taxonomy but adapted for UniProt\nhttp://www.uniprot.org/taxonomy/" [PMID:18836194]
synonym: "uniprot taxon" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[0-9]+"
xref: search-url: "http://www.uniprot.org/taxonomy/${ac}"
is_a: ??:xxxx ! region database or molecule database or experimental construct database ?

[Term]
id:
name: ncbi taxonomy
def: "The NCBI taxonomy database indexes over 55.000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group of organisms. Searches of the NCBI taxonomy may be made on the basis of whole or partial organism names, and direct links to organisms commonly used in biological research are also provided. The Taxonomy Browser can also be used to display the number of nucleic acid sequences, protein sequences, and protein structures available for organisms included in the branch. From the data display for a particular organism, one can retrieve and download the sequence data for that organism, or protein 3D structure data if available.\nhttp://www.ncbi.nlm.nih.gov/Taxonomy/" [PMID:10592169]
xref: id-validation-regexp: "[0-9]+"
xref: search-url: "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=${ac}&lvl=3&lin=f&keep=1&srchmode=1&unlock"
is_a: ??:xxxx ! region database or molecule database or experimental construct database ?

[Term]
id:
name: brenda
def: "A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.\nhttp://www.brenda-enzymes.info" [PMID:21030441]
is_a: ??:xxxx ! region database or molecule database or experimental construct database ?

[Term]
id:
name: cabri
def: "CABRI cell lines catalogue available at.\nhttp://www.cabri.org/" [PMID:31824649]
xref: id-validation-regexp: "[0-9]+|ACC\\s[A-Z0-9]+|ECACC\\s[A-Z0-9]+|LMBP\\s[A-Z0-9]+|ICLC\\s[A-Z0-9]+|CIP-[0-9]+|DSMZ_MUTZ\\:ACC\\s[0-9]+"
xref: search-url: "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id]"
is_a: ??:xxxx ! region database or molecule database or experimental construct database ?

[Term]
id:
name: cell ontology
def: "Ontology of cell types.\nhttp://obo.sourceforge.net/cgi-bin/detail.cgi?cell" [PMID:29322914]
is_a: ??:xxxx ! region database or molecule database or experimental construct database ?

[Term]
id:
name: tissue list
def: "List of tissue used as topic in UniProt RC line.\nhttp://www.expasy.org/cgi-bin/lists?tisslist.txt" [PMID:]
is_a: ??:xxxx ! region database or molecule database or experimental construct database ?

## participant db, bioactive entity reference

[Term]
id:
name: bioactive entity reference
def: "General on-line reference to other details about a drug or other bioactive entity." [PMID:]
synonym: "bioactive entity ref" EXACT PSI-ID-short []
is_a: ??:xxxx ! region database or molecule database or experimental construct database ?

[Term]
id:
name: chebi
def: "A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI).\nhttp://www.ebi.ac.uk/chebi/" [PMID:]
synonym: "ChEBI" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "CHEBI:[0-9]+"
xref: search-url: "http://www.ebi.ac.uk/chebi/searchId.do?chebiId=${ac}"
is_a: ??:xxxx ! bioactive entity reference

[Term]
id:
name: pubchem
def: "PubChem provides information on the biological activities of small molecules.\nhttp://pubchem.ncbi.nlm.nih.gov/" [PMID:16381840]
synonym: "PubChem" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! bioactive entity reference

[Term]
id:
name: chembl compound
def: "ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets." [PMID:19194660, PMID:24214965]
synonym: "chembl" EXACT []
xref: id-validation-regexp: "[0-9]+"
xref: search-url: "http://www.ebi.ac.uk/chembldb/index.php/compound/inspect/${ac}"
is_a: ??:xxxx ! bioactive entity reference
relationship: part_of ??:xxxx ! chembl

[Term]
id:
name: beilstein
def: "The Beilstein database is in the field of organic chemistry, in which compounds are uniquely identified by their Beilstein Registry Number." [PMID:ID\:11604014]
synonym: "beilstein" EXACT PSI-ID-short []
is_a: ??:xxxx ! bioactive entity reference

[Term]
id:
name: einecs
def: "The EINECS database provides general information such as CAS number, EINECS number, Substance Name and Chemical Formula for 100,204 chemical substances. Where available each compound entry is linked to risk and safety phrases and IUCLID and OECD chemical data sheets." [PMID:17125194]
synonym: "einecs" EXACT PSI-ID-short []
synonym: "European Inventory of Existing Commercial Chemical Substances " EXACT []
is_a: ??:xxxx ! bioactive entity reference

[Term]
id:
name: merck index
def: "Comprehensive information on chemicals, drugs, and biologicals." [PMID:17832605]
synonym: "merck index" EXACT PSI-ID-short []
is_a: ??:xxxx ! bioactive entity reference

[Term]
id:
name: drugbank
def: "DrugBank Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the drug's generic name. The 4 letter suffix (APRD, EXPT, BIOD, NUTR) indicates the type of drug (APRD=approved small molecule drug, EXPT=experimental drug, BIOD=biotech drug, NUTR=nutraceutical or natural product). Biotech drugs consist of FDA approved peptide, protein or nucleic acid drugs, approved small molecule drugs are FDA approved non-biotech drugs, nutraceuticals are natural products (amino acids, vitamins, other metabolites) and experimental drugs include drugs under trial, pre-clinical drugs, unapproved drugs, well known inhibitors and possible toxins." [PMID:]
is_a: ??:xxxx ! bioactive entity reference

[Term]
id:
name: cas registry number
def: "Chemical Abstract Service identification number" [PMID:]
is_a: ??:xxxx ! bioactive entity reference

[Term]
id:
name: pharmgkb
def: "Pharmacogenomics Knowledge Base identification number (if molecule is in PharmGKB)" [PMID:]
is_a: ??:xxxx ! bioactive entity reference

[Term]
id:
name: bind smid
def: "BIND database Small Molecule Identification number (if molecule is in BIND)" [PMID:]
comment: May not be publicly available any more since now owned by Thompson Scientific.
is_a: ??:xxxx ! bioactive entity reference

[Term]
id:
name: canadian drug identification number
def: "Drug Identification Number (Canadian Drug ID system)" [PMID:]
synonym: "din" EXACT PSI-ID-short []
is_a: ??:xxxx ! bioactive entity reference

[Term]
id:
name: rxlist link
def: "Hyperlink to RxList entry for the given drug (if it exists)" [PMID:]
is_a: ??:xxxx ! bioactive entity reference

[Term]
id:
name: pdr health
def: "Hyperlink to PDRhealth entry for the given drug (if it exists)" [PMID:]
synonym: "PDRhealth" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! bioactive entity reference

[Term]
id:
name: wikipedia
def: "Hyperlink to wikipedia entry for the given drug (if it exists)" [PMID:]
is_a: ??:xxxx ! bioactive entity reference

## participant db, other

[Term]
id:
name: kegg
def: "KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions.\nhttp://www.genome.ad.jp/kegg/" [PMID:10592173]
synonym: "KEGG" EXACT PSI-ID-alternate []
xref: id-validation-regexp: "[a-zA-Z]+:[a-zA-Z]+[0-9]+"
is_a: ??:xxxx ! region database or molecule database or experimental construct database ?
is_a: ??:xxxx ! pathways database

[Term]
id:
name: kegg compound
def: "Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG)" [PMID:]
synonym: "KEGG Compound ID" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! kegg

[Term]
id:
name: dflat
def: "Database dedicated to annotating gene function related to human fetal development using the Gene Ontology for functional annotation.\nhttp://bcb.cs.tufts.edu/dflat/" []
synonym: "Developmental FunctionaL Annotation at Tufts" EXACT PSI-ID-alternate []
synonym: "dflat" EXACT PSI-ID-short []
synonym: "DFLAT" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! region database or molecule database or experimental construct database ?

[Term]
id:
name: complex portal
def: "The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms, entered into the IntAct molecular interaction database . Data includes protein-only complexes as well as protein-small molecule and protein-nucleic acid complexes. All complexes are derived from physical molecular interaction evidences extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background. All complexes are tagged with Evidence and Conclusion Ontology codes to indicate the type of evidence available for each entry." [PMID:25313161]
synonym: "Complex Portal" EXACT PSI-ID-alternate []
synonym: "complex portal" EXACT PSI-ID-short []
xref: search-url: "http://www.ebi.ac.uk/complexportal/complex/${ac}"
is_a: ??:xxxx ! interaction database
is_a: ??:xxxx ! region database or molecule database or experimental construct database ?

# source database
# in PSI-MI CV this includes mainly interaction and imex databases (not included heer), as well as PDB resources (defined earlier, see feature db)
# we might want to define IDP specific source databases

[Term]
id:
name: source database
def: "Database that originally provided the IDP data record for exchange purposes." [PMID:31824649]
is_a: ??:xxxx ! database citation

[Term]
id: MI:0731
name: 3d repertoire
def: "The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository." [PMID:14755292]
synonym: "3D Repertoire" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! source database

<!-- EXPERIMENTAL PREPARATION - ROOT TERM FOR EXPERIMENTAL PREPARATION - name and xref elements of idf:experimentalPreparation element to define experimental preparation of experimental construct -->

[Term]
id:
name: experimental preparation
def: "Set of terms to describe the experimental treatment and status of the experimental region that is analysed. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each experimental region can then be annotated with a maximum of 4 terms selected from each short list." [PMID:31824649]
synonym: "experimental prep" EXACT PSI-ID-short []
relationship: part_of ID:0000 ! intrinsically disordered protein

# conformational status

[Term]
id:
name: conformational status
def: "Statement about the native/denatured conformation of the protein." [PMID:31824649]
synonym: "conformation" EXACT PSI-ID-short []
is_a: ??:xxxx ! experimental preparation

[Term]
id:
name: denatured
def: "Altered conformation state of the protein as a result of heat or chemical modification resulting in a changed structure of the protein." [PMID:31824649]
is_a: ??:xxxx ! conformational status

[Term]
id:
name: native
def: "State of the protein without interference i.e. the natural form." [PMID:31824649]
is_a: ??:xxxx ! conformational status

# delivery method
# the terms listed below have child terms that can also be taken from PSI-MI CV

[Term]
id:
name: delivery method
def: "Method by which molecule is delivered or engineered into a cell." [PMID:31824649]
is_a: ??:xxxx ! experimental preparation

[Term]
id:
name: electroporation
def: "Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm." [PMID:6329708]
is_a: ??:xxxx ! delivery method

[Term]
id:
name: infection
def: "Molecule introduced into a cell via an external organism, usually a virus or bacteria." [PMID:31824649]
is_a: ??:xxxx ! delivery method

[Term]
id:
name: microinjection
def: "The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed." [PMID:3016916]
synonym: "micro-injection" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! delivery method

[Term]
id: MI:0704
name: nucleic acid delivery
def: "Method by which nucleic acids are delivered or engineered into a cell." [PMID:31824649]
synonym: "nucl delivery" EXACT PSI-ID-short []
is_a: ??:xxxx ! delivery method

[Term]
id:
name: passive uptake
def: "Entrance of molecules into cells that does not involved specific treatments but relies on natural cellular processes." [PMID:31824649]
is_a: ??:xxxx ! delivery method

[Term]
id:
name: protein delivery
def: "Method by which proteins are delivered into a cell." [PMID:31824649]
is_a: ??:xxxx ! delivery method

# expression level

[Term]
id:
name: expression level
def: "Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell." [PMID:14755292]
is_a: ??:xxxx ! experimental preparation

[Term]
id:
name: physiological level
def: "A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate." [PMID:14755292]
synonym: "endogenous" EXACT PSI-ID-alternate []
synonym: "endogenous level" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! expression level

[Term]
id:
name: under expressed level
def: "A molecule is estimated to be expressed at lower levels than in physiological condition." [PMID:14755292]
synonym: "under-expressed" EXACT PSI-ID-short []
is_a: ??:xxxx ! expression level
is_a: ??:xxxx ! expression level alteration

[Term]
id:
name: over expressed level
def: "A molecule is estimated to be expressed at higher levels than in physiological condition." [PMID:14755292]
synonym: "over-expressed" EXACT PSI-ID-short []
is_a: ??:xxxx ! expression level
is_a: ??:xxxx ! expression level alteration

# genetic experimental form (Descriptor of an experimental form involved in a genetic interaction)
# these terms will probably not be needed in PSI-ID schema, as related to genetic interactions

# molecular source

[Term]
id:
name: molecular source
def: "Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process." [PMID:14755272]
is_a: ??:xxxx ! experimental preparation

[Term]
id:
name: engineered
def: "Molecule has been added into system from an external source or altered within the cell." [PMID:14755292]
is_a: ??:xxxx ! molecular source

[Term]
id:
name: naturally occurring
def: "Unaltered endogenous molecule in its naturally occurring state." [PMID:14755292]
synonym: "endogenous" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! molecular source

# sample process

[Term]
id:
name: sample process
def: "Indicates the sample context in which each experimental construct is presented." [PMID:14755292]
is_a: ??:xxxx ! experimental preparation

[Term]
id:
name: cdna library
def: "Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid experimental constructs not to their proteins product." [PMID:6110205]
is_a: ??:xxxx ! sample process

[Term]
id:
name: cell lysate
def: "Cell has been physically or chemically broken open and experimental construct present in resulting mixture of cellular components." [PMID:14755292]
is_a: ??:xxxx ! sample process

[Term]
id:
name: subcellular preparation
def: "Cell lysates are partially fractionated to isolate a specific subcellular fraction." [PMID:14755292]
synonym: "subcellular prep" EXACT PSI-ID-short []
is_a: ??:xxxx ! cell lysate

[Term]
id:
name: fixed cell
def: "Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis." [PMID:14755292]
is_a: ??:xxxx ! sample process

[Term]
id:
name: living cell
def: "Experimental construct is observed within in a living cell." [PMID:14755292]
is_a: ??:xxxx ! sample process

[Term]
id:
name: purified
def: "Experimental construct has undergone one or more purification steps to isolate it from the cellular environment." [PMID:14755292]
is_a: ??:xxxx ! sample process

[Term]
id:
name: homogeneous
def: "The author states an experimental construct is completely pure, i.e. no other molecular species are present." [PMID:14755292]
synonym: "pure" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! purified

[Term]
id:
name: partially purified
def: "The author states an experimental construct is only partially purified, i.e. other molecular species also known to be present." [PMID:14755292]
is_a: ??:xxxx ! purified

[Term]
id:
name: in vitro translated protein
def: "Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery." [PMID:14755292]
synonym: "in vitro translated" EXACT PSI-MI-short []
is_a: ??:xxxx ! sample process

[Term]
id:
name: conditioned medium
def: "Experimental construct present in media harvested from cultured cells." [PMID:14755292]
is_a: ??:xxxx ! sample process

[Term]
id:
name: phage library
def: "A bacteriophage library of genes encoding proteins or peptides fused to a phage coat protein that are expressed on the surface of the phage virion." [PMID:9661810]
is_a: ??:xxxx ! sample process

<!-- EXPERIMENTAL ROLE - Role played by the participant within the experiment. -->
<!-- currently we don't use/need this branch -->

<!-- INTERACTION CONFIDENCE - A method used to derive a numerical or empirical measure of confidence in a particular interaction, or in the identification of the participants in an interaction. -->
<!-- currently we don't use/need this branch -->

<!-- INTERACTION DETECTION METHOD - Method to determine the interaction. -->
<!-- currently we don't use/need this branch -->
<!-- structure determination methods will be taken from ECO -->

<!-- INTERACTOR TYPE - Molecular species involved in the interaction. -->
<!-- currently we don't use/need this branch -->
<!-- in a later version we might want to annotate type of molecules; as the PSI-MI branch is specific to species involved in an interaction, this needs to be adopted for IDP schema, or we can use a different ontology, e.g. CHEBI? -->

<!-- PARAMETER TYPE - Parameter for enzymatic or binding kinetic studies. -->
<!-- parameters in PSI-MI CV are specific for interactions, e.g. 'temperature of interaction' -->
<!-- can we use ontology of units of measure (OM) to annotate parameter types ? -->

<!-- PARAMETER UNIT - Controlled vocabulary for kinetic constant units. -->
<!-- except for the root term, available units are general, however only 4 are available in PSI-MI CV (Kelvin, molar, per mole per second, and second -->
<!-- can we use ontology of units of measure (OM) to annotate parameter units ? -->

<!-- PARTICIPANT IDENTIFICATION METHOD - Method to determine the molecules involved in the interaction. -->
<!-- if we want to annotate molecule/experimental construct/region identification methods, we can use terms from ECO CV for this? -->

<!-- BRANCH FOR FEATURE RANGE STATUS ANNOTATION HAS BEEN SLPIT OUT AND IS HERE:
https://hackmd.io/0K-K84HfQZWZ0Alb_siZHAT
-->