Header menu logo BioFSharp

Obo Module

Functions for parsing OBO terms from an OBO formatted file

Types

Type Description

DBXref

or "" {optional-trailing-modifier} The dbxref is a colon separated key-value pair. The key should be taken from GO.xrf_abbs but this is not a requirement. If provided, the dbxref description is a string of zero or more characters describing the dbxref. DBXref descriptions are rarely used and as of obof1.4 are discouraged. Dbxref lists are used when a tag value must contain several dbxrefs. Dbxref lists take the following form: [, , ...] The brackets may contain zero or more comma separated dbxref definitions. An example of a dbxref list can be seen in the GO def for "ribonuclease MRP complex": def: "A ribonucleoprotein complex that contains an RNA molecule of the snoRNA family, and cleaves the rRNA precursor as part of rRNA transcript processing. It also has other roles: In S. cerevisiae it is involved in cell cycle-regulated degradation of daughter cell-specific mRNAs, while in mammalian cells it also enters the mitochondria and processes RNAs to create RNA primers for DNA replication." [GOC:sgd_curators, PMID:10690410, Add to Citavi project by Pubmed ID PMID:14729943, Add to Citavi project by Pubmed ID PMID:7510714] Add to Citavi project by Pubmed ID Note that the trailing modifiers (like all trailing modifiers) do not need to be decoded or round-tripped by parsers; trailing modifiers can always be optionally ignored. However, all parsers must be able to gracefully ignore trailing modifiers. It is important to recognize that lines which accept a dbxref list may have a trailing modifier for each dbxref in the list, and another trailing modifier for the line itself.

OboTerm

obo term record type

OboTermDef

TermSynonym

TermSynonymScope

The value consists of a quote enclosed synonym text, a scope identifier, an optional synonym type name, and an optional dbxref list, like this: synonym: "The other white meat" EXACT MARKETING_SLOGAN [MEAT:00324, BACONBASE:03021] The synonym scope may be one of four values: EXACT, BROAD, NARROW, RELATED. If the first form is used to specify a synonym, the scope is assumed to be RELATED. The synonym type must be the id of a synonym type defined by a synonymtypedef line in the header. If the synonym type has a default scope, that scope is used regardless of any scope declaration given by a synonym tag. The dbxref list is formatted as specified in dbxref formatting. A term may have any number of synonyms.

Type something to start searching.