This R package contains EntityClass definitions that correspond to GEO Platform, Sample, and Series objects (for more information, please refer to NCBI's GEO Overview).
The GEOPlatform entity class captures GEO Platform (GPL) record fields:
| Name | Array | Type | Description |
|---|---|---|---|
| geo_accession | FALSE | Text | 'Platform_geo_accession' field of GEO record (e.g., 'GPL1234') |
| title | FALSE | Text | 'Platform_title' field of GEO record |
| manufacturer | FALSE | Text | 'Platform_manufacturer' field of GEO record |
| technology | FALSE | Text | 'Platform_technology' field of GEO record |
| organism | TRUE | Text | 'Platform_organism' field(s) of GEO record |
| taxid | TRUE | Integer | 'Platform_taxid' field of(s) GEO record |
- The
organismandtaxidvariables are array-type because a Platform record may contain more than one entry for each of these fields (i.e., a platform may include features from multiple organisms).
The GEOSample entity class captures GEO Sample (GSM) record fields and optionally refers to a CEL file:
| Name | Array | Type | Description |
|---|---|---|---|
| geo_accession | FALSE | Text | 'Sample_geo_accession' field of GEO record (e.g., 'GSM1234') |
| title | FALSE | Text | 'Sample_title' field of GEO record |
| description | TRUE | Text | 'Sample_description' field(s) of GEO record |
| type | FALSE | Text | 'Sample_type' field of GEO record |
| series_id | TRUE | Text | 'Sample_series_id' field(s) of GEO record (e.g., 'GSE1234') |
| platform_id | FALSE | Text | 'Sample_platform_id' field of GEO record (e.g., 'GPL1234') |
| data_processing | TRUE | Text | 'Sample_data_processing' field(s) of GEO record |
| channel_count | FALSE | Integer | 'Sample_channel_count' field of GEO record |
| molecule_ch1 | FALSE | Text | 'Sample_molecule_ch1' field of GEO record |
| source_name_ch1 | FALSE | Text | 'Sample_source_name_ch1' field of GEO record |
| characteristics_ch1 | TRUE | Text | 'Sample_characteristics_ch1' field(s) of GEO record |
| molecule_ch2 | FALSE | Text | 'Sample_molecule_ch2' field of GEO record |
| source_name_ch2 | FALSE | Text | 'Sample_source_name_ch2' field of GEO record |
| characteristics_ch2 | TRUE | Text | 'Sample_characteristics_ch2' field(s) of GEO record |
| affymetrixCEL | FALSE | Entity (AffymetrixCEL) | ID of an AffymetrixCEL Entity that refers to the CEL WorkFile corresponding to this Sample |
- The
description,series_id, anddata_processingvariables are array-type because a Sample record may contain more than one entry for each of these fields. - The Sample record may contain information about one or two channels, depending on the platform (the number of channels is contained in variable
channel_count). The*_ch2variables therefore may not be present in a given GEOSample record. - The
characteristicsvariables for each channel are array-type because a Sample record may contain more than one characteristics for each channel. - This record may refer to an AffymetrixCEL entity that describes a CEL WorkFile.
The GEOSample entity class captures GEO Series (GSE) record fields, refers to one or more GEOPlatform and GEOSample entities, and may optionally refer to a set of CEL files:
| Name | Array | Type | Description |
|---|---|---|---|
| geo_accession | FALSE | Text | 'Series_geo_accession' field of GEO record (e.g., 'GSE1234') |
| title | FALSE | Text | 'Series_title' field of GEO record |
| relation | TRUE | Text | 'Series_relation' field of GEO record |
| summary | TRUE | Text | 'Series_summary' field(s) of GEO record |
| type | TRUE | Text | 'Series_type' field(s) of GEO record (e.g., 'Expression profiling by array') |
| platform_id | TRUE | Text | 'Series_platform_id' field(s) of GEO record (e.g., 'GPL1234') |
| pubmed_id | TRUE | Integer | 'Series_pubmed_id' field(s) of GEO record |
| geoPlatforms | TRUE | Entity (GEOPlatform) | IDs of GEOPlatform Entities corresponding to this Series |
| geoSamples | TRUE | Entity (GEOSample) | IDs of GEOSample Entities corresponding to this Series |
| affymetrixCELSet | TRUE | Entity (AffymetrixCELSet) | IDs of AffymetrixCELSet Entities corresponding to this Series |
- The
relation,summary,type,platform_id, andpubmed_idvariables are array-type because a Series record may contain more than one entry for each of these fields. - Similarly, the entity may refer to more than one GEOPlatform (e.g., methylation and expression arrays).