mapping: Mapping table between two types of IDs

In datapplab/SBGNview.data: Supporting datasets for SBGNview package

Description

Mapping table between two types of IDs

Usage

data(ENZYME_pathway.id)

data(hsa_KO_ENTREZID)

data(mmu_KO_ENSEMBL)

data(chebi_pathway.id)

data(mmu_KO_ENTREZID)

data(chebi_compound.name)

data(compound.name_pathwayCommons)

data(kegg_pathwayCommons)

data(hsa_pathwayCommons_ENSEMBL)

data(mmu_pathwayCommons_ENTREZID)

data(KO_pathway.id)

data(KO_pathwayCommons)

data(SYMBOL_pathway.id)

data(pathwayCommons_SYMBOL)

data(chebi_pathwayCommons)

data(mmu_pathwayCommons_ENSEMBL)

data(hsa_ENTREZID_pathwayCommons)

data(chebi_kegg)

data(chebi_metacyc.SBGN)

data(compound.name_pathway.id)

data(compound.name_kegg)

Format

A matrix/data.frame with two columns: the ID mapping between two types of IDs.

An object of class data.frame with 16601 rows and 2 columns.

An object of class data.frame with 10446 rows and 3 columns.

An object of class matrix (inherits from array) with 11016 rows and 2 columns.

An object of class data.frame with 79911 rows and 2 columns.

An object of class data.frame with 11105 rows and 3 columns.

An object of class data.frame with 285207 rows and 2 columns.

An object of class data.frame with 298727 rows and 2 columns.

An object of class data.frame with 6448 rows and 2 columns.

An object of class matrix (inherits from array) with 383983 rows and 2 columns.

An object of class matrix (inherits from array) with 628413 rows and 2 columns.

An object of class data.frame with 47719 rows and 2 columns.

An object of class data.frame with 88148 rows and 2 columns.

An object of class data.frame with 252730 rows and 2 columns.

An object of class data.frame with 406940 rows and 3 columns.

An object of class matrix (inherits from array) with 60425 rows and 2 columns.

An object of class matrix (inherits from array) with 619656 rows and 2 columns.

An object of class matrix (inherits from array) with 384671 rows and 2 columns.

An object of class data.frame with 20692 rows and 2 columns.

An object of class matrix (inherits from array) with 60659 rows and 2 columns.

An object of class data.frame with 571283 rows and 2 columns.

An object of class data.frame with 61143 rows and 2 columns.

Details

Each dataset contains a mapping table. There are several types of ID pairs, such as molecule ID <=> pathway_glyph_ID, molecule ID <=> pathway ID, and molecule ID <=> KEGG ortholog ID. molecule ID <=> pathway_glyph_ID tables are extracted from Biopax files. For example: http://www.pathwaycommons.org/archives/PC3/v10/PathwayCommons10.reactome.BIOPAX.owl.gz. Glyph IDs are extracted from the ID of each XML element "Protein". Its matching molecule ID is extracted from the corresponding XML child element "UnificationXref". See more details and examples in vignette 'SBGNview.data.vignette'

datapplab/SBGNview.data documentation built on March 3, 2021, 7:34 p.m.