OBO文件中的标签的含义/意思/意义

Tags in a [Term] stanza

The OBO Flat File Format Specification, version 1.0

Required tags

id

The unique id of the current term. This can be any string. This tag must always be the first tag in any term description

Example:

id: CAR:0000001

name

The term name. Any term may only have one name defined. If multiple term names are defined, it is a parse error.

Example:

name: Volkswagen Beetle

Optional tags

alt_id

Defines an alternate id for this term. A term may have any number of alternate ids.

Example:

alt_id: CAR:0000666

namespace

The namespace in which the term belongs. If this tag is not present, the term will be assigned to the default-namespace specified in the file header stanza.

Example:

namespace: car_ontology

def

The definition of the current term. There must be zero or one instances of this tag per term description. More than one definition for a term generates a parse error. The value of this tag should be the quote enclosed definition text, followed by a dbxref list containing dbxrefs that describe the origin of this definition (see Dbxref Formatting for information on how dbxref lists are encoded).

Example:

definition: "The Volkswagen Beetle or Bug is a small family car, the best known car of Volkswagen, of Germany, and almost certainly the world. Thanks to its distinctive shape and sound, its reliability, and presumably other factors, it now enjoys a cult status." [http://en.wikipedia.org/ "Wikipedia", VW:0283 ""]

comment

A comment for this term. There must be zero or one instances of this tag per term description. More than one comment for a term generates a parse error.

Example:

comment: Note that this term refers to both the old and new (post-1998) Beetles.

subset

This tag indicates a term subset to which this term belongs. The value of this tag must be a subset name as defined in a subsetdef tag in the file header. If the value of this tag is not mentioned in a subsetdef tag, a parse error will be generated. A term may belong to any number of subsets.

Example:

subset: classic_cars

synonym

This tag gives a synonym for the term; whether the synonym is exact, broad, narrow, or otherwise related to the term is not specified. The value of this tag should be the quote enclosed synonym text, followed by an optional dbxref list containing dbxrefs that describe the origin of this synonym (see Dbxref Formatting for information on how dbxref lists are encoded). A term may have any number of synonyms.

Example:

synonym: "The Bug" [VEH:391840]

related_synonym
exact_synonym
broad_synonym
narrow_synonym

These tags give a synonym for the term of the specified type; see the documentation on synonyms for information on synonym types. The value of the tag should be the quote enclosed synonym text, followed by an optional dbxref list containing dbxrefs that describe the origin of this synonym (see Dbxref Formatting for information on how dbxref lists are encoded). A term may have any number of related synonyms.

Example:

exact_synonym: "VW Bug" [VW:0283, TPT:938VWB]
related_synonym: "Type 1" []

xref_analog

A dbxref that describes an analogous object in another vocabulary (see Dbxref Formatting for information about how the value of this tag must be formatted). A term may have any number of analogous xrefs.

Example:

xref_analog: VW:0283

xref_unknown

A dbxref with an unknown type (see Dbxref Formatting for information about how the value of this tag must be formatted). A term may have any number of unknown typed xrefs. This tag should not be used if possible (see Parser Requirements for information about how parsers may handle this tag).

is_a

This tag describes a subclassing relationship between one term and another. A term may have any number of is a relationships. Terms with no is a relationships are roots. A term with no is a relationships may not specify any relationship tags. To do so is a parse error.

Example:

is_a: CAR:0009478

relationship

This tag describes a typed relationship between this term and another term. The value of this tag should be the relationship type id, and then the id of the target term. The relationship type name must be a relationship type name as defined in a typedef tag stanza. The typedef must either occur in a document in the current parse batch, or in a file imported via a typeref header tag. If the relationship type name is undefined, a parse error will be generated. If the id of the target term cannot be resolved by the end of parsing the current batch of files, this tag describes a "dangling reference". See Parser Requirements for information about how a parser may handle dangling references. If a relationship is specified for a term with an is_obsolete value of true, a parse error will be generated. If a relationship target is a term which is obsolete, a parse error will be generated.

Example:

relationship: part_of CAR:0009478

is_obsolete

This tag indicates whether or not the term is obsolete. Allowable values are "true" and "false" (false is assumed if this tag is not present). Obsolete terms must have no relationship or is_a tags.

Example:

is_obsolete: true

use_term

This tag indicates which term to use instead of an obsolete term. The value of this tag is the id of another term. If the tag value refers to a term that is not specified in the current load batch, it is a "dangling reference" (see Parser Requirements). If this tag is specified and the is_obsolete value for the current term is not true, a parse error will be generated. This tag is not required for terms that specify the is_obsolete tag, but it is recommended (some parsers may choose to issue warnings about obsolete terms that do not specify a replacement term). An obsolete term may have any number of use_term tags.

domain

This tag determines the children that can be assigned to relationships with this type. If the domain is set, term relationships with this type may only have children that are the same as, or subclasses of, the domain term.

Note: This tag is not used in GO at present, although it is available for use in OBO-formatted files for any ontology.

range

This tag specifies the parents that can be assigned to relationships with this type. If the range is set, term relationships with this type may only have parents that are the same as, or subclasses of, the range term.

Note: This tag is not used in GO at present, although it is available for use in OBO-formatted files for any ontology.

from  http://www.geneontology.org/GO.format.obo-1_0.shtml

is_cyclic

This tag indicates that it is legal to create cycles out of this relationship.

Note: This tag is not used in GO at present, although it is available for use in OBO-formatted files for any ontology.

is_transitive

This tag indicates that the relationship is marked as transitive. This information is very useful to reasoners and other automatic traversals of the graph.

Note: This tag is not used in GO at present, although it is available for use in OBO-formatted files for any ontology.

is_symmetric

This tag indicates that the relationship is marked as symmetric (meaning that if the relationship holds from the child to parent, it also holds from parent to child). This information is very useful to reasoners and other automatic traversals of the graph.

Note: This tag is not used in GO at present, although it is available for use in OBO-formatted files for any ontology.