This section of the HTML version of the ontology contains the
class definitions of the ontology. Each class defines a type of
entity. A class is defined to have a set of slots, where each slot
defines attributes and properties that may be used by an instance of
that class.
Slots are inherited by a class from its parent classes. Usually this
HTML form of the ontology shows only the names of the slots at each
class, with links provided to the full definition of the slot in the
slot section of the ontology. However, when the definition of a slot
is changed within a class with respect to its parent, the full
definition of the slot is shown.
The Evidence class defines a controlled vocabulary of evidence types. Each term in the vocabulary
defines a type of evidence that pertains to an assertion in this database. Example assertions include
the assertion that a pathway exists, or the assertion that an operon exists. Example uses of the
evidence vocabulary are to record what type of evidence supports the assertion that an operon exists,
such as whether the evidence is based on a computational analysis or a wet-lab experiment, and if the
latter, what type of wet-lab experiment.
COMMENT: The Evidence class defines a controlled vocabulary of evidence types. Each term in the vocabulary
defines a type of evidence that pertains to an assertion in this database. Example assertions include
the assertion that a pathway exists, or the assertion that an operon exists. Example uses of the
evidence vocabulary are to record what type of evidence supports the assertion that an operon exists,
such as whether the evidence is based on a computational analysis or a wet-lab experiment, and if the
latter, what type of wet-lab experiment.
Author statement. The evidence for an assertion comes from an author
statement in a publication, where that publication does not state direct experimental support
for the assertion. Ordinarily, this code will not be used directly -- generally one of
its child codes, EV-TAS or EV-NAS, will be used instead.
COMMENT: Author statement. The evidence for an assertion comes from an author
statement in a publication, where that publication does not state direct experimental support
for the assertion. Ordinarily, this code will not be used directly -- generally one of
its child codes, EV-TAS or EV-NAS, will be used instead.
Author hypothesis. The hypothesis is in a publication, but it was clearly indicated in the
publication that there was no experimental evidence, or limited evidence, supporting the
hypothesis. This code can be used, for example, for "paper chemistry" metabolic pathways,
which are pathways drawn from the author's best estimation.
COMMENT: Author hypothesis. The hypothesis is in a publication, but it was clearly indicated in the
publication that there was no experimental evidence, or limited evidence, supporting the
hypothesis. This code can be used, for example, for "paper chemistry" metabolic pathways,
which are pathways drawn from the author's best estimation.
Non-traceable author statement. The assertion was made in a publication such as a review, a meeting abstract,
or another database without a reference to a publication describing an experiment that supports the assertion.
COMMENT: Non-traceable author statement. The assertion was made in a publication such as a review, a meeting abstract,
or another database without a reference to a publication describing an experiment that supports the assertion.
Traceable author statement. The assertion was made in a publication -- such as a review or
in another database -- that itself did not describe an experiment supporting the
assertion. The statement referenced another publication that supported the assertion,
but it is unclear whether that publication described an experiment that supported
the assertion. The difference between the codes EV-EXP-TAS and EV-AS-TAS
is that the former code is used when it is certain that experimental evidence supports the
assertion, and the latter code is used when there is a possibility that an experiment was
not done to support the assertion.
In general, references to the primary literature are preferred,
but this code can be used when the original article is difficult to locate.
COMMENT: Traceable author statement. The assertion was made in a publication -- such as a review or
in another database -- that itself did not describe an experiment supporting the
assertion. The statement referenced another publication that supported the assertion,
but it is unclear whether that publication described an experiment that supported
the assertion. The difference between the codes EV-EXP-TAS and EV-AS-TAS
is that the former code is used when it is certain that experimental evidence supports the
assertion, and the latter code is used when there is a possibility that an experiment was
not done to support the assertion.
In general, references to the primary literature are preferred,
but this code can be used when the original article is difficult to locate.
Inferred from computation. The evidence for an assertion comes from a
computational analysis. The assertion itself might have been made
by a person or by a computer, that is, EV-COMP does not specify whether
manual interpretation of the computation occurred.
COMMENT: Inferred from computation. The evidence for an assertion comes from a
computational analysis. The assertion itself might have been made
by a person or by a computer, that is, EV-COMP does not specify whether
manual interpretation of the computation occurred.
Automated inference. A computer inferred this assertion through one of many possible methods such as
sequence similarity, recognized motifs or consensus sequence, etc. When a person made the inference
from computational evidence, use EV-HINF
COMMENT: Automated inference. A computer inferred this assertion through one of many possible methods such as
sequence similarity, recognized motifs or consensus sequence, etc. When a person made the inference
from computational evidence, use EV-HINF
COMMON-NAME: Inferred computationally without human oversight
Automated inference of function from sequence. A computer inferred a gene function based on sequence,
profile, or structural similarity (as computed from sequence) to one or more other sequences.
COMMENT: Automated inference of function from sequence. A computer inferred a gene function based on sequence,
profile, or structural similarity (as computed from sequence) to one or more other sequences.
COMMON-NAME: Automated inference of function from sequence
Automated inference of transcription unit based on single-gene directon. Existence of a single-gene transcription unit
for gene G is inferred computationally by the existence of upstream and downstream genes transcribed in the
opposite direction of G.
COMMENT: Automated inference of transcription unit based on single-gene directon. Existence of a single-gene transcription unit
for gene G is inferred computationally by the existence of upstream and downstream genes transcribed in the
opposite direction of G.
COMMON-NAME: Automated inference that a single-gene directon is a transcription unit
Human inference. A curator or author inferred this assertion after review of one or more possible types
of computational evidence such as sequence similarity, recognized motifs or consensus sequence, etc.
When the inference was made by a computer in an automated fashion, use EV-AINF.
COMMENT: Human inference. A curator or author inferred this assertion after review of one or more possible types
of computational evidence such as sequence similarity, recognized motifs or consensus sequence, etc.
When the inference was made by a computer in an automated fashion, use EV-AINF.
COMMON-NAME: Inferred by a human based on computational evidence
A person inferred, or reviewed a computer inference of, gene function based
on sequence, profile, or structural similarity (as computed from sequence) to
one or more other sequences.
COMMENT: A person inferred, or reviewed a computer inference of, gene function based
on sequence, profile, or structural similarity (as computed from sequence) to
one or more other sequences.
COMMON-NAME: Human inference of function from sequence
There exists physical evidence of the binding of cellular extracts containing
a regulatory protein to its DNA binding site. This can be either by
footprinting or mobility shift assays.
COMMENT: There exists physical evidence of the binding of cellular extracts containing
a regulatory protein to its DNA binding site. This can be either by
footprinting or mobility shift assays.
Sites or genes bounding the transcription unit are experimentally identified. Several possible cases exist, such as defining the boundaries of a transcription unit with an experimentally identified promoter and terminator, or with a promoter and a downstream gene that is transcribed in the opposite direction, or with a terminator and an upstream gene that is transcribed in the opposite direction.
COMMENT: Sites or genes bounding the transcription unit are experimentally identified. Several possible cases exist, such as defining the boundaries of a transcription unit with an experimentally identified promoter and terminator, or with a promoter and a downstream gene that is transcribed in the opposite direction, or with a terminator and an upstream gene that is transcribed in the opposite direction.
COMMON-NAME: Boundaries of transcription experimentally identified
Direct assay of partially purified protein from a specific organism.
Protein partially purified, and activity measured using an in vitro
assay. Expression host is unspecified.
COMMENT: Direct assay of partially purified protein from a specific organism.
Protein partially purified, and activity measured using an in vitro
assay. Expression host is unspecified.
Direct assay of protein partially purified from a heterologous
host. Recombinant protein partially purified
from a heterologous host expressing cloned gene(s), and activity
measured using an in vitro assay.
COMMENT: Direct assay of protein partially purified from a heterologous
host. Recombinant protein partially purified
from a heterologous host expressing cloned gene(s), and activity
measured using an in vitro assay.
COMMON-NAME: Assay of protein partially-purified from a heterlogous host
Direct assay of protein partially purified from its native
host. Protein partially purified from its
native host, and activity measured using an in vitro assay.
COMMENT: Direct assay of protein partially purified from its native
host. Protein partially purified from its
native host, and activity measured using an in vitro assay.
COMMON-NAME: Assay of protein partially-purified from its native host
COMMENT: Direct assay of purified protein. Protein purified to homogeneity, and
activity measured using an in vitro assay. Expression host is unspecified.
COMMON-NAME: Assay of protein purified to homogeneity
Direct assay of protein purified from a heterologous host. Recombinant
protein purified to homogeneity from a heterologous host expressing
cloned gene(s), and activity measured using an in vitro assay.
COMMENT: Direct assay of protein purified from a heterologous host. Recombinant
protein purified to homogeneity from a heterologous host expressing
cloned gene(s), and activity measured using an in vitro assay.
COMMON-NAME: Assay of protein purified to homogeneity from a heterlogous host
Direct assay of protein purified from its native host. Protein
purified to homogeneity from its native host, and activity measured
using an in vitro assay.
COMMENT: Direct assay of protein purified from its native host. Protein
purified to homogeneity from its native host, and activity measured
using an in vitro assay.
COMMON-NAME: Assay of protein purified to homogeneity from its native host
Protein purified from mixed culture or other multispecies environment (such as, infected plant or animal tissue), and activity measured through in vitro assay.
COMMENT: Protein purified from mixed culture or other multispecies environment (such as, infected plant or animal tissue), and activity measured through in vitro assay.
COMMON-NAME: Assay of protein purified from mixed culture
The length of the (transcribed) RNA is experimentally determined. The length of the mRNA is compared with that of the DNA sequence and by this means the number of genes transcribed are established.
COMMENT: The length of the (transcribed) RNA is experimentally determined. The length of the mRNA is compared with that of the DNA sequence and by this means the number of genes transcribed are established.
COMMON-NAME: Length of transcript experimentally determined
Direct assay of unpurified protein. Presence of a protein activity is
indicated by an assay, but the protein has not been purified.
Expression host is unspecified.
COMMENT: Direct assay of unpurified protein. Presence of a protein activity is
indicated by an assay, but the protein has not been purified.
Expression host is unspecified.
Direct assay of unpurified protein from a heterologous host. Presence
of a newly acquired protein activity is indicated by an assay
performed on a heterologous host expressing recombinant
protein(s). The recombinant proteins have not been purified.
COMMENT: Direct assay of unpurified protein from a heterologous host. Presence
of a newly acquired protein activity is indicated by an assay
performed on a heterologous host expressing recombinant
protein(s). The recombinant proteins have not been purified.
COMMON-NAME: Assay of unpurified protein expressed in a heterlogous host
Direct assay of unpurified protein from its native host. Presence of a
protein activity is indicated by an assay performed with an organism,
but the precise identity of the protein responsible for that activity
is not established, since the protein has not been purified.
COMMENT: Direct assay of unpurified protein from its native host. Presence of a
protein activity is indicated by an assay performed with an organism,
but the precise identity of the protein responsible for that activity
is not established, since the protein has not been purified.
COMMON-NAME: Assay of unpurified protein expressed in its native host
Inferred through co-regulation. A transcription unit is inferred because a set of
adjacent genes that are transcribed in the same direction exhibit similar
expression patterns under a range of environmental conditions.
COMMENT: Inferred through co-regulation. A transcription unit is inferred because a set of
adjacent genes that are transcribed in the same direction exhibit similar
expression patterns under a range of environmental conditions.
The expression of the gene is analyzed through a transcriptional fusion (i.e. lacZ), and a difference in expression levels is observed when the regulatory protein is present (wild type) vs in its absence. Note that this evidence does not eliminate the possiblity of an indirect effect of the regulator on the regulated gene.
COMMENT: The expression of the gene is analyzed through a transcriptional fusion (i.e. lacZ), and a difference in expression levels is observed when the regulatory protein is present (wild type) vs in its absence. Note that this evidence does not eliminate the possiblity of an indirect effect of the regulator on the regulated gene.
IGI inferred from genetic interaction.
The assertion was inferred from a genetic interaction such as
"Traditional" genetic interactions such as suppressors, synthetic lethals, etc.
Functional complementation
Inference about one gene drawn from the phenotype of a mutation in a different gene
This category includes any combination of alterations in the sequence
(mutation) or expression of more than one gene/gene product. This
category can therefore cover any of the IMP experiments that are done
in a non-wild-type background, although we prefer to use it only when
all mutations are documented. When redundant copies of a gene must all
be mutated to see an informative phenotype, use the IGI code. (Yes,
this implies some organisms, such as mouse, will have far, far more IGI
than IMP annotations.)
IMP also covers phenotypic similarity: a phenotype that is informative
because it is similar to that of another independent phenotype (which
may have been described earlier or documented more fully) is IMP (not IGI).
We have also decided to use this category for situations where a
mutation in one gene (gene A) provides information about the function,
process, or component of another gene (gene B; i.e. annotate gene B
using IGI).
COMMENT: IGI inferred from genetic interaction.
The assertion was inferred from a genetic interaction such as
"Traditional" genetic interactions such as suppressors, synthetic lethals, etc.
Functional complementation
Inference about one gene drawn from the phenotype of a mutation in a different gene
This category includes any combination of alterations in the sequence
(mutation) or expression of more than one gene/gene product. This
category can therefore cover any of the IMP experiments that are done
in a non-wild-type background, although we prefer to use it only when
all mutations are documented. When redundant copies of a gene must all
be mutated to see an informative phenotype, use the IGI code. (Yes,
this implies some organisms, such as mouse, will have far, far more IGI
than IMP annotations.)
IMP also covers phenotypic similarity: a phenotype that is informative
because it is similar to that of another independent phenotype (which
may have been described earlier or documented more fully) is IMP (not IGI).
We have also decided to use this category for situations where a
mutation in one gene (gene A) provides information about the function,
process, or component of another gene (gene B; i.e. annotate gene B
using IGI).
COMMENT: Protein activity inferred by isolating its gene and performing functional complementation of a well characterized heterologous mutant for the protein.
COMMON-NAME: Inferred by functional complementation
IMP inferred from mutant phenotype.
The assertion was inferred from a mutant phenotype such as
Any gene mutation/knockout
Overexpression/ectopic expression of wild-type or mutant genes
Anti-sense experiments
RNA interference experiments
Specific protein inhibitors
Complementation
Comment: Inferences made from examining mutations or
abnormal levels of only the product(s) of the gene of interest are covered by code EV-IMP
(compare to code EV-IGI). Use this code for experiments that use antibodies
or other specific inhibitors of RNA or protein activity, even though no
gene may be mutated (the rationale is that EV-IMP is used where an
abnormal situation prevails in a cell or organism).
COMMENT: IMP inferred from mutant phenotype.
The assertion was inferred from a mutant phenotype such as
Any gene mutation/knockout
Overexpression/ectopic expression of wild-type or mutant genes
Anti-sense experiments
RNA interference experiments
Specific protein inhibitors
Complementation
Comment: Inferences made from examining mutations or
abnormal levels of only the product(s) of the gene of interest are covered by code EV-IMP
(compare to code EV-IGI). Use this code for experiments that use antibodies
or other specific inhibitors of RNA or protein activity, even though no
gene may be mutated (the rationale is that EV-IMP is used where an
abnormal situation prevails in a cell or organism).
If a mutation in a gene or promoter prevents expression of the downstream genes due to a polar effect, the mutated gene is clearly part of the transcription unit.
COMMENT: If a mutation in a gene or promoter prevents expression of the downstream genes due to a polar effect, the mutated gene is clearly part of the transcription unit.
A cis-mutation in the DNA sequence of the transcription-factor binding site interferes with the operation of the regulatory function. This is considered strong evidence for the existence and functional role of the DNA binding site.
COMMENT: A cis-mutation in the DNA sequence of the transcription-factor binding site interferes with the operation of the regulatory function. This is considered strong evidence for the existence and functional role of the DNA binding site.
IPI inferred from physical interaction
The assertion was inferred from a physical interaction such as
2-hybrid interactions
Co-purification
Co-immunoprecipitation
Ion/protein binding experiments
This code covers physical interactions between the gene product of
interest and another molecule (or ion, or complex). For functions such
as protein binding or nucleic acid binding, a binding assay is
simultaneously IPI and IDA; IDA is preferred because the assay
directly detects the binding. For both IPI and IGI, it would be good
practice to qualify them with the gene/protein/ion.
COMMENT: IPI inferred from physical interaction
The assertion was inferred from a physical interaction such as
2-hybrid interactions
Co-purification
Co-immunoprecipitation
Ion/protein binding experiments
This code covers physical interactions between the gene product of
interest and another molecule (or ion, or complex). For functions such
as protein binding or nucleic acid binding, a binding assay is
simultaneously IPI and IDA; IDA is preferred because the assay
directly detects the binding. For both IPI and IGI, it would be good
practice to qualify them with the gene/protein/ion.
Traceable author statement to experimental support. The assertion was made in a publication -- such as a review or
in another database -- that itself did not describe an experiment supporting the
assertion. However, the statement did reference another publication describing an experiment
that supports the assertion. The difference between the codes EV-EXP-TAS and EV-AS-TAS
is that the former code is used when it is certain that experimental evidence supports the
assertion, and the latter code is used when there is a possibility that an experiment was
not done to support the assertion.
In general, references to the primary literature are preferred,
but this code can be used when the original article is difficult to locate.
COMMENT: Traceable author statement to experimental support. The assertion was made in a publication -- such as a review or
in another database -- that itself did not describe an experiment supporting the
assertion. However, the statement did reference another publication describing an experiment
that supports the assertion. The difference between the codes EV-EXP-TAS and EV-AS-TAS
is that the former code is used when it is certain that experimental evidence supports the
assertion, and the latter code is used when there is a possibility that an experiment was
not done to support the assertion.
In general, references to the primary literature are preferred,
but this code can be used when the original article is difficult to locate.
COMMON-NAME: Traceable author statement to experimental support
A transcription unit is inferred because there is a set of adjacent genes,
encoded in the same direction, coding for products that participate in the
same metabolic pathway or biological process. Sometimes, these genes code
for subunits of the same protein.
COMMENT: A transcription unit is inferred because there is a set of adjacent genes,
encoded in the same direction, coding for products that participate in the
same metabolic pathway or biological process. Sometimes, these genes code
for subunits of the same protein.
COMMON-NAME: Products of adjacent genes in the same biological process
This section of the HTML version of the ontology contains the
slot definitions of the ontology. Each slot itself has several
properties such as documentation about that slot, a cardinality
(specifying the number of values that the slot may have), a value type
(specifying the data type of slot values), and a domain (specifying
the class(es) in which the slot is used).
The primary name by which an object is known to
scientists. Typically the name will be a standard name, or a widely used and familiar name.
In some cases arbitrary choices must be made when picking the Common-Name.
This slot lists the one or more classes that this evidence code pertains to. For example, some evidence codes pertain to promoters only. If no class is listed, we assume the evidence code pertains to all classes of objects.
COMMON-NAME: Pertains-To
QUERYABLE?: T
DOMAIN: Evidence