Pheno-XML
Chris Mungall 2006
The RNC is the master version -
RNG and XSD is autogenerated from RNC
A document consists of some combination of genotypes and
phenotypes, manifestations of phenotypes via genotypes, and
genetic features
: File format version :
should match this schema version (eg 0.01)
[
SO type. "gene" for mutant allele. May also be some
kind of sequence_variant (eg deletion, P_insertion, SNP)
defaults to SO:gene (ie an allele)
]
[
may be from genetic context ontology
e.g. dominant, codominant
]
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
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
[
free text summary of the entire phenotype manifestation;
]
[
genotypes of the individual or individuals that
show the phenotype.
]
[
The collection of characteristics exhibited in this
manifestation
]
[
support or evidence; experimental details
]
[
there is an implicit 'normal' environment
if multiple environments are specified, the association
holds for ALL of them
]
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.
[
An identifier for a phenotype term. If supplied, this would
come from a full
ontology of pre-coordinated phenotype terms such as MP or
the plant_trait ontology
]
[
free text summary of the phenotype character
]
[
the type of entity in which the qualities inhere
can be a process type or continuant type
]
[
the quality types (attributes, properties) that are the
hallmarks of this character
]
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)
[
qualities can be borne by processes or continuants;
the bearer can thus be drawn from GO process, component,
or from an ontology of cells or larger anatomical entities.
]
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.
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)
[
quality type. comes from PATO
]
[
optional free text
]
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
[
for relative qualities we may want an explicit "yardstick"
]
[
not all phenotype characters can be specified in
qualitative terms using classes from an ontology of
quality states. Sometimes unit-based quantitative measurements
must be used - for example, weight in kg
rather than overloading the 'type' field we treat measurements
separately. Measurements complement quality space annotations;
a phenotype character can be both "shorter_than" wild-type
and also 2cm in length. Either or both of these can be
specified in the annotation
]
[
Qualities can change over time: a quality may instantiate 'hot' at one time and 'cold' at a later time.
we may know the exact time stage (eg larval to pupal), or we may have an open range (eg post-larval), repeated
ranges..
multiple qualifiers can be specified (eg before t2 and after t1)
if no qualifiers are specified then there is no implied time - it is assumed to happen at some point
in the organisms life time, UNLESS it is constrained by the bearer bearer type.
for example, if the bearer is "larva" then the attached state occurs during the larval stage. for this
to be infered, the appropriate relations must be specified in the anatomical ontology
]
[
What the quality type would be in wild-type, or
whatever the comparison target is. Can specify multiple
values if these are exhibited by the target.
for example, if color is red or pink in wildtype, then
we can specify these two here.
specifying target types can lead to redundancy, this
is only required when for example our canonical
anatomical ontologies are not specific w.r.t quality types
]
[
What typical measurements would be in wild-type, or
whatever the comparison target is. Can specify multiple
values if these are exhibited by the target
]
for abnormal/normal
these should come from the PATO modifier terminology
[
We can post-compose references to more detailed types
for which no defined term exists
]
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"
[
The interval may be typed by a term/class from an ontology of
developmental stages, processes or life cycles.
]
[
an OPTIONAL measurement of the time; eg in seconds, hours,
years, etc. Measured either from when the particular attribute
(and hence bearer) came into existence, or in absolute time.
]
an optionally-attributed textual description
e.g pubmed ID