Unified Medical Language System® (UMLS®)
2015AB UMLS Gene Ontology Source Information
This page lists specific source data elements and provides information on their representation in the UMLS Metathesaurus.
NotesGO "terms" are analagous to the Metathesaurus idea of "descriptors," i.e. a collection of closely related but not necessarily synonymous names. In the documentation below, the word "Term" is used in the the GO sense of the word in order to describe the original GO data in the language used by the source itself.
Summary of Changes:)
Source-Provided Files: Summary( )
Data files in various formats and extensive documentation is available at: http://www.geneontology.org/
Documentation and Reference
|http://oboformat.googlecode.com/svn/trunk/doc/GO.format.obo-1_2.html||OBO format documentation|
|gene_ontology_ext_20150404.obo||OBO data file|
* Certain fields and data elements may not be directly processed because they contain redundant data.
Source-Provided Files: Details( )
In OBO, content is structured as tag-value pairs, with optional trailing modifiers. Tag-value pairs consist of a tag name, an unescaped colon, the tag value, and a newline.
Consult the GO OBO format documentation for additional details.
For inclusion in the Metathesaurus, all tags in a [Term] Stanza, are processed, as described in the OBO format documentation.Required tags:
|id||Unique identifier||MRCONSO.CODE, MRCONSO.SDUI|
TTY = "PT" if there is no is_obsolete flag
TTY = "OP" if is_obsolete = true
|namespace||Ontology (domain) name. Valid values are:
|MRSAT.ATN = "GO_NAMESPACE"
Optional tags: the following table lists only tags actually present in the data processed for inclusion in this version of the Metathesaurus. Tags are presented in the order in which they appear in a [Term] Stanza. For information on all optional OBO tags, including deprecated tags, please consult the OBO format documentation.
|alt_id||Alternate identifier||MRSAT.ATN = "SID"|
|comment||Comment||MRSAT.ATN = "GO_COMMENT"|
|subset||Subset. Valid values are:
|MRSAT.ATN = "GO_SUBSET"|
TTYs are assigned based on the value of the scope identifier and the presence or absence of the "is_obsolete" tag.
REL values are assigned based on the value of the scope identifier
Optional dbxref lists included in synonym tags are represented in MRSAT.ATN = "REF"
When present on "EXACT" synonyms, the modifier "systematic_synonym" is represented in MRSAT.ATN ="SYN_QUALIFIER," MRSAT.ATV="systematic_synonym"
|xref||Cross-reference (dbxref) describing an analagous term in another vocabulary||MRSAT.ATN = "GXR"|
|is_a||Indicates a subclassing relationship between one term and another||Used to create a hierarchy, represented in MRHIER.RRF and MRREL.RRF (REL = "PAR," "CHD," "SIB"; RELA = "isa")|
|relationship||Describes a relationship between one term and another.
Valid values are:
For part_of, MRREL.REL = "RN/RB"
For all other relationship tag values, MRREL.REL = "RO"
|is_obsolete||Indicates if a term is obsolete||Used to compute termtype assignments|
|replaced_by||Gives a term which replaces an obsolete term||MRREL.REL = "RO"
MRREL.RELA = "replaced_by/replaces"
|consider||Gives a term which may be an appropriate substitute or an obsolete term, but requires human review||MRREL.REL = "RO"
MRREL.RELA = "consider/consider_from"
|disjoint_from||Indicates that a term is disjoint from another, meaning that the two terms have no instances or subclasses in common. The value is the id of the term from which the current term is disjoint.||MRSAT.ATN = "DISJOINT_FROM"|
|intersection_of||Indicates that this term is equivalent to the intersection of several other terms. The value is either a term id, or a relationship type id, a space, and a term id.||If the value is a GO term id: MRREL.REL = "RN/RB";
MRREL.RELA = "isa/inverse_isa"
If the value includes a relationship type: MRREL.REL and MRREL.RELA are populated appropriately based on the value of the relationship type. Relationship groups are used tolink pairs (or groups) of intersecting relationship.
|creation_date||Indicates the creation time and date of the term||MRSAT.ATN = "DATE_CREATED"|