Namespace: http://www.bioontologies.org/obd/schema/pheno
A document consists of some combination of genotypes and phenotypes, manifestations of phenotypes via genotypes, and genetic features
| version | Built-in type string | optional |
|---|---|---|
|
: File format version : should match this schema version (eg 0.01) | ||
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
Each genotype record represents a single individual or group of genetically similar individuals
| id | Simple type pheno:identifier_Type | optional |
|---|---|---|
| organism | Simple type pheno:identifier_Type | optional |
|
NCBI TAxon ID | ||
| background | Simple type pheno:identifier_Type | optional |
|
another genotype | ||
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
Simple type pheno:name_Type
Namespace: http://www.bioontologies.org/obd/schema/pheno
A genotype is a collection of alleles In general, only the mutant alleles are specified. sequence variants can also be specified
| copy_count | Built-in type int | optional |
|---|---|---|
| feature | Simple type pheno:identifier_Type | optional |
|
a reference to a genetic feature | ||
Empty
Namespace: http://www.bioontologies.org/obd/schema/pheno
A genetic feature may be a gene (allele), transcript, SNP, etc typed by SO This is a partial model of genetic features - a full model can be found in Chado
| id | Simple type pheno:identifier_Type | required |
|---|---|---|
|
unique stable global identifier - this can be used to reference more detailed info in a sequence/genetics db | ||
| organism | Simple type pheno:identifier_Type | optional |
|
optional: same as genotype.organism_id if not specified | ||
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
a single genotype can be associated with multiple phenotypes in different experiments and different environments
| penetrance_percentage | Built-in type float | optional |
|---|---|---|
| genotype | Simple type pheno:identifier_Type | optional |
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
A phenotype manifestation is an observation of a phenotype in one more individual organisms under experimental conditions, linked with the genetic and environmental causes of that phenotype
| id | Simple type pheno:identifier_Type | optional |
|---|---|---|
|
Each manifestation can be identified, but this is optional. Note that the ID is for the manifestation of the phenotype in either a single individual organism, or in a population of indistinguishable individuals in an experiment or trial | ||
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
a phenotype is a collection of characteristics possessed by an organism or collection of organisms (or in some cases, the environment of the organism, as a result of that organism's actions - for example a termite's nest) the phenotype arises as a result of the organism's genotype and the environment of the organism Examples of phenotypes are: * "red eyes and notched wings" * "reduced apoptosis and increased susceptibility to cancer" * "Initially a single lateral is formed, but it is thicker than normal and sometimes individual bundles of actin filaments can be seen. The laterals split near the distal tip as they elongate and at later stages they appear to be split over more of their length." * "interrupted imaginal disc development and stunted wings at the adult stage" The phenotype is the entire collection of characteristics exhibited by that organism (or collection of effectively indistinguishable organsisms). Each organism has a single phenotype throughout its lifespan - the characteristics that comprise that phenotype may change, this is reflected in the phenotype_character records each phenotype record represents a specific phenotype which may be instantiated in one or more organisms. If two or more organisms have indistinguishable phenotypes, the same record may be used. If phenotypes are distinguishable then a different record should be used.
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
A phenotype character is one or more qualities inhering in a single bearer entity. For example, a PC with quality type "red" and bearer type "eye" (written here for convenience as "red eye") represents a particular instantiation of "red eye"/"red eyes" in a particular organism or collection of like organisms examples of phenotype character types: red hair, low bone mass, square jaw, long thick bristle, 2cm long tail, spermatocyte devoid of asters, elevated blood pressure, lacking wings, having an additional digit relative to a wild type individual, having a brain size during embryonic development that is larger than a typical individual of the same genus/order, short attention span, having an abnormal shape, abnormal fusion between digits, lacking red spots, abnormally low numbers of B-cells after infection, lacking circularity in the cross-section of an arista lateral A phenotype character record represents an instance of a characteristic possessed by a single organism, or a collection of identical characteristics possessed by like organisms.
| id | Simple type pheno:identifier_Type | optional |
|---|---|---|
| expressivity_percentage | Built-in type float | optional |
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
each 'bearer' record represents a particular bearer of some general bearer type: for example, a particular wing of a particular fly entities can be spatial objects (3D e.g. anatomical parts) or spatiotemporal entities (4D e.g. processes)
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
aka attribute aka property any one particular bearer can have multiple qualities inhering in it. For example, a particular tail can have qualities such as shape, length, etc each quality inheres in a single bearer throughout the duration of that entities existence. For example, my height is a single quality that inheres in my body throughout my life. This quality can take on different states throughout the lifetime of the bearer.
| determinable | Simple type pheno:classId_Type | optional |
|---|---|---|
|
not required: it can be deduced from the quality type. if provided, the value of this field is always an OBO-style identifier from PATO may be useful for report purposes; eg the color of this entity is red (where 'color' is the determinable) | ||
| count | Built-in type integer | optional |
|
certain kinds of quality implicitly or explicitly refer to numbers. Examples of these are the qualities of "having supernumery parts" or the qualities of "lacking parts". It can be useful to state the exact number here, rather than overloading the ontology of qualities. the number will refer to either the relative or absolute quantity....? This is purely optional, as it is usually sufficient to state that a particular hand has supernumery fingers, without saying how many extra | ||
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
Relational qualities inhere in additional entities. This should be used for relational qualities (e.g. sensitivity, distance_from) and not for monadic entities. other examples include: "spermatocytes *devoid_of* asters", "thorax *lacks* wing", hand *has-supernumerary-parts* finger in these cases, the related_entity records the _type_ of part that is lacking or present in lower or higher numbers
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
sometimes a state is only instantiated if a certain condition holds
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
quality types can be absolutist (square, red) or relative (high pressure, short height). relative always implies a context. The default context is always an equivalent phenotype character in a typical individual of the same species. We can be more explicit if we like by specifying in_comparison_to Examples: an allele which has more or less pronounced effects in different genetic backgrounds; A yellow eye which is red in wildtype;
| relation | Simple type pheno:classId_Type | optional |
|---|---|---|
|
if left blank, this is inferred from the quality type; for example, if Q="high pressure", then the relation is higher-than or increased-with-respect-to | ||
| about | Simple type pheno:identifier_Type | optional |
|
Can be an ID of a particular phenotype manifestation, or an ID for a whole taxon | ||
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
for abnormal/normal these should come from the PATO modifier terminology
| about | Simple type pheno:classId_Type | required |
|---|---|---|
Empty
Namespace: http://www.bioontologies.org/obd/schema/pheno
: measurement : examples: length measurement (with ruler, in cm) spot intensity real-world measurements (exlcuding count measurements) are inexact and hence ranges.
| unit | Built-in type NMTOKEN | required |
|---|---|---|
|
the unit should be a reference to an SI unit Q: do SI units have an identifier system, or do we just use eg "mm" Q: do we need the ability to specify composite units, eg lb/kg - or is this handled by SI? | ||
| value | Built-in type float | optional |
|
the only time this would be omitted is if we only have a range | ||
| min_value | Built-in type float | optional |
|
Q: does the range reflect our lack of knowledge (eg accuracy of measuring instrument) or an actual range of values? or should we represent an actual range as multiple measurements? | ||
| max_value | Built-in type float | optional |
| standard_deviation | Built-in type float | optional |
| standard_error | Built-in type float | optional |
| assay | Simple type pheno:identifier_Type | optional |
|
TODO: reference to a particular experiment | ||
Empty
Namespace: http://www.bioontologies.org/obd/schema/pheno
evidence: could refer to papers, figures in papers, raw images, etc
| id | Simple type pheno:identifier_Type | required |
|---|---|---|
| type | Simple type pheno:classId_Type | optional |
Empty
Namespace: http://www.bioontologies.org/obd/schema/pheno
The type of environment. For now this is just a pre or post coordinated type reference. In future We may want to add more under here
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
A reference to a type. Here type is used in the ontology sense of a "kind" or "universal". A type can be referenced simply by giving a term ID from an ontology. More complex types can be "post-coordinated"
| about | Simple type pheno:classId_Type | required |
|---|---|---|
|
Base/generic type. This is often all that is required. the ID is OBO-compliant and can be from any ontology | ||
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
for cross-products these are the characteristics that distinguish a specific type from a general type e.g. if we want to annotate to an bearer "scutum bristle" and the anatomical ontology does not contain this term, only "scutum" and "bristle". In this case the bearer type_id (ie the primary term) would be the ID for "bristle". We would have one differentium "part_of scutum"
| relation | Simple type pheno:classId_Type | required |
|---|---|---|
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
temporal_qualifier examples: during larval stage; after pupal stage; at 7pm on 2000/01/01; overlapping M1-phase; we do not tie ourself to any one theory of time - time ranges and points are represented using time_range
| relation | Simple type pheno:classId_Type | optional |
|---|---|---|
|
e.g. before, after, during - would come from an ontology of temporal relations this is optional. If not specified, treated as *overlap* relation | ||
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
represents an interval or point in time (we are neutral w.r.t points vs intervals)
| id | Simple type pheno:identifier_Type | optional |
|---|---|---|
|
: id : OPTIONAL this is typically not used. You would use it if you wish to grant an identifier to a particular time point or range. This would allow you to make partial-order statements; e.g. t1 before t2 | ||
Exactly 1 sequences of:
Namespace: http://www.bioontologies.org/obd/schema/pheno
an optionally-attributed textual description
| id | Built-in type NMTOKEN | optional |
|---|---|---|
| attribution | Simple type pheno:identifier_Type | optional |
|
e.g pubmed ID | ||
Built-in type string
Built-in type string
Built-in type NMTOKEN