All the possible values for columns
and keytypes
are listed
below. Users will have to actually use these methods to learn which
of the following possible values actually apply in their case.
- ACCNUM:
- GenBank accession numbers
- ALIAS:
- Commonly used gene symbols
- ARACYC:
- KEGG Identifiers for arabidopsis as indicated by aracyc
- ARACYCENZYME:
- Aracyc enzyme names as indicated by aracyc
- CHR:
- Chromosome (deprecated for Bioc > 3.1) For this
information you should look at a TxDb or OrganismDb object and
search for an appropriate field like TXCHROM, EXONCHROM or
CDSCHROM. This information can also be retrieved from these objects
using an appropriate range based accesor like transcripts,
transcriptsBy etc.
- CHRLOC:
- Chromosome and starting base of associated gene
(deprecated for Bioc > 3.1) For this information you should look at
a TxDb or OrganismDb object and search for an appropriate field like
TXSTART etc. or even better use the associated range based accessors
like transcripts or transcriptsBy to get back GRanges objects.
- CHRLOCEND:
- Chromosome and ending base of associated gene
(deprecated for Bioc > 3.1) For this information you should look at
a TxDb or OrganismDb object and search for an appropriate field like
TXEND etc. or even better use the associated range based accessors
like transcripts or transcriptsBy to get back GRanges objects.
- COMMON:
- Common name
- DESCRIPTION:
- The description of the associated gene
- ENSEMBL:
- The ensembl ID as indicated by ensembl
- ENSEMBLPROT:
- The ensembl protein ID as indicated by ensembl
- ENSEMBLTRANS:
- The ensembl transcript ID as indicated by ensembl
- ENTREZID:
- Entrez gene Identifiers
- ENZYME:
- Enzyme Commission numbers
- EVIDENCE:
- Evidence codes for GO associations with a gene of interest
- EVIDENCEALL:
- Evidence codes for GO (includes less specific terms)
- GENENAME:
- The full gene name
- GO:
- GO Identifiers associated with a gene of interest
- GOALL:
- GO Identifiers (includes less specific terms)
- INTERPRO:
- InterPro identifiers
- IPI:
- IPI accession numbers
- MAP:
- cytoband locations
- OMIM:
- Online Mendelian Inheritance in Man identifiers
- ONTOLOGY:
- For GO Identifiers, which Gene Ontology (BP, CC, or MF)
- ONTOLOGYALL:
- Which Gene Ontology (BP, CC, or MF), (includes less specific terms)
- ORF:
- Yeast ORF Identifiers
- PATH:
- KEGG Pathway Identifiers
- PFAM:
- PFAM Identifiers
- PMID:
- Pubmed Identifiers
- PROBEID:
- Probe or manufacturer Identifiers for a chip package
- PROSITE:
- Prosite Identifiers
- REFSEQ:
- Refseq Identifiers
- SGD:
- Saccharomyces Genome Database Identifiers
- SMART:
- Smart Identifiers
- SYMBOL:
- The official gene symbol
- TAIR:
- TAIR Identifiers
- UNIGENE:
- Unigene Identifiers
- UNIPROT:
- Uniprot Identifiers
To get the latest information about the date stamps and source URLS
for the data used to make an annotation package, please use the
metadata method as shown in the example below.
Unless otherwise indicated above, the majority of the data for any one
package is taken from the source indicated by either it's name (if
it's an org package) OR from the name of it's associated org package.
So for example, org.Hs.eg.db is using "eg" in the name to indicate
that most of the data in that package comes from NCBI entrez gene
based data. And org.At.tair.db uses data that primarily comes from
tair. For chip packages, the relevant information is the organism
package that they depend on. So for example, hgu95av2.db depends on
org.Hs.eg.db, and is thus primarily based on NCBI entrez gene ID
information.