LOCUSID	LocusLink identifier	"This is an R environment (hash table like) object containing key and value pairs for the mappings between  probe identifiers (key) and LocusLink ids (values). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given probe identifier can be mapped to only one or more LocusLink ids. NA is assigned to probe identifiers that can not be mapped to a LocusLink id at this time.  "	LL	Y
CURRENTLOCUSID	Previous LocusLink id if merged	This is an R environment object containing key and value pairs for the mappings between probe identifiers (key) and current locus ids (values). Keys can be accessed using R ls and values using get or multiget command. Values may be vectors of length 1 or greater depending on whether a given probe identifier can be mapped to only one or more current locus ids. NA is assigned to probe identifiers that can not be mapped to a current locus id at this time. 	LL	Y
LOCUSTYPE	Type of locus	This is an R environment object containing key and value pairs for the mappings between  probe identifiers (key) and  locus type (values). Keys can be accessed using R ls and values using get or multiget command. Values may be vectors of length 1 or greater depending on whether a given probe identifier can be mapped to only one or more locus type. NA is assigned to probe identifiers that can not be mapped to a locus type at this time. 	LL	Y
NG	RefSeq accession for genomic region records	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and the RefSeq accession for genomic region (nucleotide) records (value). Keys can be accessed using ls (name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given probe id can be mapped to only one or more RefSeq accession for genomic region records. NA is used for probe ids that can not be mapped to a RefSeq accession for genomic region records at this time. "	LL	Y
NM	RefSeq accession for a mRNA record	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and the RefSeq accession for a mRNA record (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given probe id can be mapped to only one or more RefSeq accession for a mRNA record. NA is used for probe ids that can not be mapped to a RefSeq accession for a mRNA record at this time. "	LL	Y
NC	Accession for chromosome RefSeq records	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and the accession for chromosome RefSeq records (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given probe id can be mapped to only one or more accession for chromosome RefSeq records. NA is used for probe ids that can not be mapped to an accession for chromosome RefSeq records at this time. "	LL	Y
NP	RefSeq accession for a protein record	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and the RefSeq accession for a protein record (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given probe id can be mapped to only one or more RefSeq accessions for a protein record. NA is used for probe ids that can not be mapped to a RefSeq accession for a protein record at this time. "	LL	Y
PRODUCT	Name of the product of transcript.	This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and the name of the product of transcript of the underlying gene (value). Keys can be accessed using ls and values using get or multiget. Values may be vectors of length 1 or greater depending on whether a given probe id can be mapped to only one or more products. NA is used for probe ids that can not be mapped to a product at this time. 	LL	Y
ACCNUM	GenBank accession number	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and GenBank accession numbers (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget (keys, name of the environment). Values are vectors of length 1. NA is assigned to probe identifiers that can not be mapped to a GenBank accession number. Mappings between probe ids and GenBank accession numbers are assumed to be provided by users. "	LL	Y
SYMBOL	Symbol used for gene reports	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and gene symbols (value), which are symbols used to report genes. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1. Mappings between probe ids and gene symbols were obtained through their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be mapped to any gene symbol at this time. "	LL	Y
GENENAME	Gene Description used for gene reports	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and gene names (value), which are  descriptions used for gene reports. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of  length 1. Mappings between peobe ids and gene names were obtained through their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be mapped to any gene name at this time. "	LL	Y
SUMMARY	A summary description of the gene	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and gene summaries (value), which are descriptions of genes, their products, significances, and mutant phenotypes. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1. Mappings between probe ids and summaries were obtained through their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be mapped to any summary at this time. "	LL	Y
UNIGENE	UniGene cluster identifier associated with a gene	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and UniGene cluster ids (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment) . Values may be vectors of length 1 or greater depending on whether a given probe identifier can be mapped to only one or more UniGene cluster ids. Mappings between probe ids and UniGene ids were obtained through their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be mapped to any UniGene cluster id at this time."	LL	Y
CHR	Chromosome assignment	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and the chromosome the corresponding genes reside (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1. Mappings between probe ids and chromosome name were obtained through their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be mapped to any chromosome at this time. "	LL	Y
MAP	Cytoband location of gene 	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and cytoband locations (value) on a chromosome. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1. Mappings between probe ids and cytoband locations were obtained through their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be mapped to any cytoband at this time. "	LL	Y
PMID	PubMed unique identifier	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and PubMed ids (value), which are subsets of publications associated with the underlying genes corresponding to the probe ids. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given probe identifier can be mapped to only one or more publications. Mappings between probe ids and PubMed ids were obtained through their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be mapped to any publication at this time. "	LL	Y
GRIF	PubMed unique identifier	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and the unique PubMed ids (value) of the publication reporting the genes corresponding to the probe ids. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1. Mappings between probe ids and GRIF ids were obtained through their mappings to LocusLink ids.  NA is assigned to probe identifiers that can not be mapped to any unique PubMed id. "	LL	Y
SUMFUNC	A brief summary of the function of the products of a gene	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and summaries of the function (value), which are brief descriptions of the functions of the products of genes. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1. Mappings between probe ids and descriptions of functions were obtained through their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be mapped to any summary of function at this time.  "	LL	Y
GO	Gene Ontology identifier	"This is an R environment (hash table lilke) object containing key and value pairs for the mappings between probe identifiers (key) and Gene Ontology information collected from Gene Ontology consortium. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Each probe id is mapped to a list of one (mapped to none or one GO id) or more (mapped to more than one GO ids) elements. When a probe id is mapped to at lest one GO id, each element of the list contains a sub list of three elements named ""GOID"", ""Ontology"", and ""Evidence"". Values for element ""GOID"" gives the Gene Ontology identifiers the key probe ids corresponding to. Values for element ""Ontology"" can be an abbreviation of MF (mocular function), BP (biological process), or CC (cellular component) for the GO category the GO id belongs to. Values for element ""Evidence"" contains an evidence code indicating what kind of evidence is found to support the association of the GO id to the key probe id. The evidence codes in use include:  
\item{IMP}{inferred from mutant phenotype}  
\item{IGI}{inferred from genetic interaction}
\item{IPI}{inferred from physical interaction}  
\item{ISS}{inferred from sequence similarity} 
\item{IDA}{inferred from direct assay}  
\item{IEP}{inferred from expression pattern}  
\item{IEA}{inferred from electronic annotation}  
\item{TAS}{traceable author statement}  
\item{NAS}{non-traceable author statement}  
\item{ND}{no biological data available}  
\item{IC}{inferred by curator}  
Mappings between probe ids and GO ids were obtained through their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be mapped to any Gene Ontology id at this time. Mappings between Gene Ontology ids an Gene Ontology terms and other information are available in a separate data package named GO. "	LL	Y
OMIM	MIM (Mendelian Inheritance in Man) number	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and MIM (Mendelian Inheritance in Man) number . Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1 or greater depending on whether a given probe identifier can be mapped to only one or MIM numbers. Mappings between probe ids and OMIMids were obtained through their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be mapped to any MIM number at this time."	LL	Y
CHRLOC	Chromosomal location 	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and transcription startting  positions of genes on chromosomes (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are named vectors of length 1 or more depending on whether a given probe id can be mapped to a single or multiple chromosomes. The names give the chromosome number of concern. NA is assigned to probe identifiers that can not be mapped to any chromosomal location data at this time. Starting positions for genes on the antisense strand have a leading ""-"" sign (e. g. -1234567). The starting positions for both the sense and antisense strand are number of base pairs measured from the p (5' end of the sense strand) to q (3' end of the sense strand) arms.  When a gene can not be placed on a chromosome with confidence, ""random"" is appended to the end of the name for a chromosomal location value. Mappings were obtained using refLint.txt.gz and refGene.txt.gz file from Golden Path (\url{http://www.genome.ucsc.edu/goldenPath/}) from the latest release."	GP	Y
CHRORI	Chromosomal orientation	"This is an R environment object containing key and value pairs for the mappings between probe identifiers (key) and chromosomal orientation of genes (value). Keys can be accessed using ls(name) and values using get(key, name) or multiget(keys, name). Values are named vectors of length 1 or more depending on whether a given probe id can be mapped to a single or multiple chromosomes. The names give the chromosome number of concern. NA is assigned to probe identifiers that can not be mapped to any chromosomal orientation data at this time. Mappings are obtained using data from LocusLink (www.ncbi.nlm.nih.gov/LocusLink) and Human Genome Project (http://genome.cse.ucsc.edu/goldenPath) based on unified mappings between probe identifiers and LocusLink ids and LocusLink ids and gene locations.  "	GP	Y
PATH	KEGG pathway identifier	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and pathway identifiers defined by KEGG (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given probe identifier can be associated with only one or more pathways. Mappings between probe ids and pathway ids were obtained their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be  associated with any pathway at this time. Mappings between pathway ids to pathway names can be found in a separate data package named KEGG. "	KEGG	Y
ENZYME	Enzyme commission number	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and Enzyme Commission numbers (value) with the leading EC: portion omitted. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given probe identifier can be associated with only one or more enzyme ids. Mappings between probe ids and enzyme ids were obtained their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be  associated with any enzyme id at this time."	KEGG	Y
BPPARENTS	GO ids of the immediate parents under biological process	"This is an R environment (hash table like) object containing key and value pairs for the mappings between GO ids and the GO ids of their direct parents (nodes directly linked to but above the GO ids along the directed acyclic graph defined by GO) under biological process (BP). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are named vectors of length 1 or greater depending on whether a given GO id has only one or more direct parents. The name(s) of value(s) is(are) the association code (isa or partof) between the GO id and its direct parents. Biological process is defined as the broad biological goals, such as mitosis or purine metabolism, that are accomplished by ordered assemblies of molecular functions as defined by Gene Ontology Consortium.  "	GO	N
CCPARENTS	GO ids of the immediate parents under cellular component	"This is an R environment (hash table like) object containing key and value pairs for the mappings between GO ids and the GO ids of the direct parents (nodes directly linked to but above the GO ids along the directed acyclic graph defined by GO) under cellular component(CC). Keys can be accessed using ls(name of the environment) and values using get (key, name of the environment) or multiget(keys, name of the environment). Values are named vectors of length 1 or greater depending on whether a given GO id has only one or more direct parents. The name(s) of value(s) is(are) the association code (isa or partof) between the GO id and its direct parents. Cellular component is defined as the subcellular structures, locations, and macromolecular complexes; examples include nucleus, telomere, and origin recognition complex as defined by Gene Ontology Consortium. "	GO	N
MFPARENTS	GO ids of the immediate parents under molecular function	"This is an R environment (hash table like) object containing key and value pairs for the mappings between GO ids and GO ids of the direct parents (nodes directly linked to but above the GO ids along the directed acyclic graph defined by GO) under molecular function(MF). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are named vectors of length 1 or greater depending on whether a given GO id has only one or more direct parents. The name(s) of value(s) is(are) the association code (isa or partof) between the GO id and its direct parents. Molecular function is defined as the tasks performed by individual gene products; examples are transcription factor and DNA helicase as defined by Gene Ontology Consortium. "	GO	N
BPCHILDREN	GO ids of the immediate children under biological process	"This is an R environment (hash table like) object containing key and value pairs for the mappings between GO ids and the GO ids of the direct (nodes directly linked to but below the GO ids along the directed acyclic graph defined by GO) children under biological process (BP). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given GO id has only one or more children. Biological process is defined as the broad biological goals, such as mitosis or purine metabolism, that are accomplished by ordered assemblies of molecular functions as defined by Gene Ontology Consortium. "	GO	N
CCCHILDREN	GO ids of the immediate children under cellular component	"This is an R environment (hash table like) object containing key and value pairs for the mappings between GO ids and the GO ids of the direct (nodes directly linked to but below the GO ids along the directed acyclic graph defined by GO) children under cellular component(CC). Keys can be accessed using ls(name of the environment) and values using get(name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given GO id has only one or more direct children. Cellular component is defined as the subcellular structures, locations, and macromolecular complexes; examples include nucleus, telomere, and origin recognition complex as defined by Gene Ontology Consortium. "	GO	N
MFCHILDREN	GO ids of the immediate children under molecular function	"This is an R environment (hash table like) object containing key and value pairs for the mappings between GO ids and the GO ids of the direct (nodes directly linked to but below the GO ids along the directed acyclic graph defined by GO) children under cellular component (CC). Keys can be accessed using ls(name fo the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given GO id has only one or more direct children. Molecular function is defined as the tasks performed by individual gene products; examples are transcription factor and DNA helicase as defined by Gene Ontology Consortium.  "	GO	N
CATEGORY	"The category (MF, BP, CC) a GO id belongs to"	"This is an R environment (hash table like) object containing key and value pairs for the mappings between GO ids and the ontology category defined by Gene Ontology Consortium namely molecular function (MF), biological process(BP), and cellular component(CC). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1 that can be GO (gene ontology top level), MF, BP, or CC. "	GO	N
PATH2PROBE	Mappings between KEGG pathway id and probe id	"This is an R environment (hash table like) object containing key and value pairs for the mappings between KEGG pathway ids and probe identifiers. Keys can be accessed using ls(name fo the environment) and values using get(keys, name of the environment) or multiget(key, name of the environment). Values may be vectors of length 1 or greater depending on whether a given pathway id can be mapped to only one or more probe identifiers. Pathway ids can not be mapped to a probe identifier are assigned a value NA. "	KEGG	N
ENZYME2PROBE	Mappings between Enzyme Commission number and probe id.	"This is an R environment (hash table like) object containing key and value pairs for the mappings between Enzyme Commission numbers (key) and probe identifiers (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given Enzyme Commission number can be mapped to only one or more probe identifiers. Enzyme Commission numbers can not be mapped any an probe identifier are assigned a value NA. GO terms corresponding to a given Enzyme Commission number can be obtained through another environment (KEGGENZYMEID2GO) in data package KEGG. "	KEGG	N
PMID2PROBE	Mappings between PubMed id and probe id	"This is an R environment (hash table like) object containing key and value pairs for the mappings between PubMed ids (key) and probe identifiers (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given PubMed id can be mapped to only one or more probe identifiers. PubMed ids can not be mapped to any probe identifier are assigned a value NA. "	LL	N
ONTOLOGY	Ontology term defined by Gene Ontology Consortium	"This is an R environment (hash table like) object containing key and value pairs for the mappings between GO ids(key) and GO ontology terms (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1.  "	GO	Y
PROBECOUNTS	Counts of probes	"This is an R environment object containing key and value pairs for the mappings between GO ids (key) and counts of probe identifiers (value) that are associated with the GO id and its direct children. Keys can be accessed using ls(name) and values using get(key, name) or multiget(keys, name). Values are vectors of length 1. GO ids that do not have any count is assigned a value NA. "	LL	N
GO2PROBE	Mappings between GO id and probe id	"This is an R environment (hash table like) object containing key and value pairs for the mappings between Gene Ontology ids (key) and probe identifiers (value), which are the probe identifiers that are associated with the corresponding GO id directly or indirectly through the children of the GO id. Values may be vectors of length 1 or greater depending on whether a given GO id can be mapped to only one or more probe identifiers. Names for values are the evidence codes for the GO ids (if evidence code was provided by source data). The evidence codes in use include:  
\item{IMP}{inferred from mutant phenotype}  
\item{IGI}{inferred from genetic interaction}
\item{IPI}{inferred from physical interaction}  
\item{ISS}{inferred from sequence similarity}  
\item{IDA}{inferred from direct assay}  
\item{IEP}{inferred from expression pattern}  
\item{IEA}{inferred from electronic annotation}  
\item{TAS}{traceable author statement}  
\item{NAS}{non-traceable author statement}  
\item{ND}{no biological data available}  
\item{IC}{inferred by curator}  O ids can not be mapped to any probe identifier are assigned a value of NA. Mappings between Gene Ontology ids an Gene Ontology terms and other information are available in a separate data package named GO. "	LL	N
GO2ALLPROBES	Mappings between GO id and probe id belonging to a GO id and its parents	"This is an R environment (hash table like) object containing key and value pairs for the mappings between Gene Ontology ids (key) and probe identifiers (value) associated with a given GO id and all the offspring of that GO id. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given GO id can be mapped to only one or more probe identifiers. Names for values are the evidence codes for the GO ids (if evidence code was provided by source data). The evidence codes in use include:  
\item{IMP}{inferred from mutant phenotype}  
\item{IGI}{inferred from genetic interaction}
\item{IPI}{inferred from physical interaction}  
\item{ISS}{inferred from sequence similarity}  
\item{IDA}{inferred from direct assay}  
\item{IEP}{inferred from expression pattern}  
\item{IEA}{inferred from electronic annotation}  
\item{TAS}{traceable author statement}  
\item{NAS}{non-traceable author statement}  
\item{ND}{no biological data available}  
\item{IC}{inferred by curator} GO ids can not be mapped to any probe identifier is assigned a value of NA. Mappings between Gene Ontology ids an Gene Ontology terms and other information are available in a separate data package named GO. "	LL	N
LL2GO	Mappings between LocusLink id to GO ids	"This is an R environment (hash table like) object containing key and value pairs for the mappings between LocusLink id (key) and Gene Ontology identifiers (value) defined by Gene Ontology consortium. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are named vectors of length 1 or greater depending on whether a given LocusLink id can be mapped to only one or more Gene Ontology ids. Names for values are the evidence codes for the GO ids (if evidence code was provided by source data). The evidence codes in use include:  
\item{IMP}{inferred from mutant phenotype}  
\item{IGI}{inferred from genetic interaction}
\item{IPI}{inferred from physical interaction}  
\item{ISS}{inferred from sequence similarity}  
\item{IDA}{inferred from direct assay}  
\item{IEP}{inferred from expression pattern}  
\item{IEA}{inferred from electronic annotation}  
\item{TAS}{traceable author statement}  
\item{NAS}{non-traceable author statement}  
\item{ND}{no biological data available}  
\item{IC}{inferred by curator}   NA is assigned to LocusLink id that can not be mapped to any Gene Ontology id at this time. Mappings between Gene Ontology ids an Gene Ontology terms and other information are available in a separate data package named GO. "	LL	N
GO2ALLLL	Mappings between GO ids to LocusLink ids	"This is an R environment (hash table like) object containing key and value pairs for the mappings between Gene Ontology id (key) and all the LocusLink ids (value) corresponding to the GO id and its offsprings. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are named vectors of length 1 or greater depending on whether a given Gene Ontology id can be mapped to only one or more LocusLink ids. Names for values are the evidence codes for the GO id (if evidence code was provided by source data). The evidence codes that are in use include:  
\item{IMP}{inferred from mutant phenotype}  
\item{IGI}{inferred from genetic interaction}
\item{IPI}{inferred from physical interaction}  
\item{ISS}{inferred from sequence similarity}  
\item{IDA}{inferred from direct assay}  
\item{IEP}{inferred from expression pattern}  
\item{IEA}{inferred from electronic annotation}  
\item{TAS}{traceable author statement}  
\item{NAS}{non-traceable author statement}  
\item{ND}{no biological data available}  
\item{IC}{inferred by curator}  NA is assigned to Gene Ontology id that can not be mapped to any LocusLink id at this time. Mappings between Gene Ontology ids an Gene Ontology terms and other information are available in a separate data package named GO. "	LL	N
GO2LL	Mappings between GO ids to LocusLink ids	"This is an R environment (hash table like) object containing key and value pairs for the mappings between Gene Ontology id (key) and LocusLink ids (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are named vectors of length 1 or greater depending on whether a given Gene Ontology id can be mapped to only one or more LocusLink ids. Names for values are the evidence codes for the GO id (if evidence code was provided by source data). The evidence codes that are in use include:  
\item{IMP}{inferred from mutant phenotype}  
\item{IGI}{inferred from genetic interaction}
\item{IPI}{inferred from physical interaction}  
\item{ISS}{inferred from sequence similarity}  
\item{IDA}{inferred from direct assay}  
\item{IEP}{inferred from expression pattern}  
\item{IEA}{inferred from electronic annotation}  
\item{TAS}{traceable author statement}  
\item{NAS}{non-traceable author statement}  
\item{ND}{no biological data available}  
\item{IC}{inferred by curator}  NA is assigned to Gene Ontology id that can not be mapped to any LocusLink id at this time. Mappings between Gene Ontology ids an Gene Ontology terms and other information are available in a separate data package named GO. "	LL	N
PATHID2EXTID	Mappings between KEGG pathway ids to External ids	"This is an R environment (hash table like) object containing key and value pairs for the mappings between KEGG pathway ids (key) and External ids (value). KEGG pathway ids are the identifiers used by KEGG for various pathways and external ids include LocusLink ids for human, mouse, and rat and Open Reading Frame ids for yeast. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1 or greater depending on whether a given KEGG pathway id can be mapped to only one or more external ids.  NA is assigned to KEGG pathway ids that can not be mapped to any external id. This environment is intended to be used for the retrieval of all the LocusLink ids for human, mouse, and rat and the Open Reading Frame ids for yeast for a given pathway id. Mappings between KEGG pathway ids and pathway names can be obtained through another environment named PATHID2NAME. "	KEGG	N
EXTID2PATHID	Mappings between External ids to KEGG pathway ids	"This is an R environment (hash table like) object containing key and value pairs for the mappings between External ids (key) and KEGG pathway ids(value). External ids include LocusLink ids for human, mouse, and rat and Open Reading Frame ids for yeast. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1 or greater depending on whether a given external id can be mapped to only one or more KEGG pathway ids.  NA is assigned to external ids that can not be mapped to any pathway id. KEGG pathway ids are the identifiers used by KEGG for various pathways. Mappings between KEGG pathway ids and pathway names can be obtained through another environment named PATHID2NAME. "	KEGG	N
PATHID2NAME	Mappings between KEGG pathway id and pathway name	"This is an R environment (hash table like) object containing key and value pairs for the mappings between KEGG pathway ids and pathway names. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1.  Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to pathway names using pathway ids as the linkages. "	KEGG	N
ENZYMEID2NAME	Mappings between Enzyme Commission number and enzyme name	"This is an R environment (hash table like) object containing key (enzyme id) and value (enzyme name) pairs for the mappings between Enzyme Commission number and Enzyme names. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1.  Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to enzyme names using Enzyme Commission numbers as the linkages."	KEGG	N
PATHNAME2ID	Mappings between KEGG pathway name to pathway id	"This is an R environment (hash table like) object containing key (path name) and value (path id) pairs for the mappings between KEGG pathway names and pathway ids. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1.  Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to pathway names using pathway ids as the linkages."	KEGG	N
ENZYMEID2GO	Mappings between Enzyme Commission id and GO id	"This is an R environment (hash table like) object containing key (enzyme id) and value (GO id) pairs for the mappings between Enzyme Commission numbers and Gene Ontology terms. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1. Enzyme Commission numbers that can not be mapped to a GO term are assigned a value NA.  Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to GO term using Enzyme Commission numbers as the linkages."	KEGG	N
GO2ENZYMEID	Mappings between GO id and Enzyme Commission id	"This is an R environment (hash table like) object containing key (GO id) and value (enzyme id) pairs for the mappings between Gene Ontology terms and Enzyme Commission numbers. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1. GO terms can not be mapped to an probe identifier are assigned a value NA.  Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to Enzyme Commission numbers using GO terms as the linkages or vice versa."	KEGG	N
GO2EVIDENCE	Mappings between GO id and evidence code provided by LocusLink	"This is an R environment object containing key and value pairs for the mappings between GO ids and evidence codes provided by LocusLink. Keys can be accessed using ls(name) and values using get(key, name) or multiget(keys, name). Values are vectors of length 1 or more depending on whether one or more evidence codes are provided to  given GO id. GO ids with no evidence code provided are assigned a value NA. "	LL	N
BPANCESTOR	Mappings between GO id and GO ids of the ancestors of the GO id	"This is an R environment (hash table like) object containing key and value pairs for the mappings between Gene Ontology ids and the GO ids of all the ancestors of the key GO id under biological process defined by Gene Ontology Consortium. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are lists of length 1 or more depending on whether the key GO id has one or more ancestor cohorts. The first element of the list contains a vector of GO ids for all the direct parents, the second element of the list contains a vectors of GO ids for all the grand parents, and so on. Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to GO ids of all the ancestors using GO ids as the linkages."	GO	N
MFANCESTOR	Mappings between GO id and GO ids of the ancestors of the GO id	"This is an R environment (hash table like) object containing key and value pairs for the mappings between Gene Ontology ids and the GO ids of all the ancestors of the key GO id under mocular function defined by Gene Ontology Consortium. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are lists of length 1 or more depending on whether the key GO id has one or more ancestor cohorts. The first element of the list contains a vector of GO ids for all the direct parents, the second element of the list contains a vectors of GO ids for all the grand parents, and so on. Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to GO ids of all the ancestors using GO ids as the linkages."	GO	N
CCANCESTOR	Mappings between GO id and GO ids of the ancestors of the GO id	"This is an R environment (hash table like) object containing key and value pairs for the mappings between Gene Ontology ids and the GO ids of all the ancestors of the key GO id cellular component defined by Gene Ontology Consortium. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are lists of length 1 or more depending on whether the key GO id has one or more ancestor cohorts. The first element of the list contains a vector of GO ids for all the direct parents, the second element of the list contains a vectors of GO ids for all the grand parents, and so on. Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to GO ids of all the ancestors using GO ids as the linkages."	GO	N
CCOFFSPRING	Mappings between GO id and GO ids of the ancestors of the GO id	"This is an R environment (hash table like) object containing key and value pairs for the mappings between Gene Ontology ids and the GO ids of all the offsprings of the key GO id cellular component defined by Gene Ontology Consortium. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are lists of length 1 or more depending on whether the key GO id has one or more offspring cohorts. The first element of the list contains a vector of GO ids for all the direct children, the second element of the list contains a vectors of GO ids for all the grand children, and so on. Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to GO ids of all the offsprings using GO ids as the linkages."	GO	N
MFOFFSPRING	Mappings between GO id and GO ids of the ancestors of the GO id	"This is an R environment (hash table like) object containing key and value pairs for the mappings between Gene Ontology ids and the GO ids of all the offsprings of the key GO id under mocular function defined by Gene Ontology Consortium. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are lists of length 1 or more depending on whether the key GO id has one or more offspring cohorts. The first element of the list contains a vector of GO ids for all the direct children, the second element of the list contains a vectors of GO ids for all the grand children, and so on. Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to GO ids of all the offsprings using GO ids as the linkages."	GO	N
BPOFFSPRING	Mappings between GO id and GO ids of the ancestors of the GO id	"This is an R environment (hash table like) object containing key and value pairs for the mappings between Gene Ontology ids and the GO ids of all the offsprings of the key GO id under biological process defined by Gene Ontology Consortium. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are lists of length 1 or more depending on whether the key GO id has one or more offspring cohort. The first element of the list contains a vector of GO ids for all the direct children, the second element of the list contains a vectors of GO ids for all the grand children, and so on. Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to GO ids of all the offsprings using GO ids as the linkages."	GO	N
BPID2TERM	Mappings between GO id and GO term under biological process	"This is an R environment (hash table like) object containing key and values pairs for the mappings between Gene Ontology ids and the corresponding GO terms under biological process defined by Gene Ontology Consortium. Keys can be accessed using ls(name) and values using get(key, name) or multiget(keys, name). Values are vectors of length 1. All the obsolete GO terms are under the node ""obsolete biological process"" with a GO id of GO:0008371. Each of the GO ids is a direct child of GO:0008371. Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to GO terms using GO ids as the linkages."	GO	N
CCID2TERM	Mappings between GO id and GO term under cellular component	"This is an R environment (hash table like) object containing key and values pairs for the mappings between GO ids and the corresponding GO terms under cellular component defined by Gene Ontology Consortium. Keys can be accessed using ls(name) and values using get(key, name) or multiget(keys, name). Values are vectors of length 1. All the obsolete GO terms are under the node ""obsolete cellular component"" with a GO id GO:0008370. Each of the GO ids is a direct child of GO:0008370. Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to GO terms using GO ids as the linkages."	GO	N
MFID2TERM	Mappings between GO id and GO term under molecular function	"This is an R environment (hash table like) object containing key and values pairs for the mappings between GO ids and the corresponding GO terms under molecular function defined by Gene Ontology Consortium. Keys can be accessed using ls(name) and values using get(key, name) or multiget(keys, name). Values are vectors of length 1. All the obsolete GO terms are under the node ""obsolete molecular function with a GO id GO:0008369.  Each of the DO ids is a direct child of GO:0008369. Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to GO terms using GO ids as the linkages."	GO	N
TERM	Mappings between GO id and GO term	"This is an R environment (hash table like) object containing key and values pairs for the mappings between GO ids and the corresponding GO terms defined by Gene Ontology Consortium. Keys (GO ids) can be accessed using ls(GOTERM) and values (GO terms) using get(key, GOTERM) or multiget(keys, GOTERM). Values are name vectors of length 1. Names of the vectors indicating the GO category a term belongs to (MF = mocular function, BP = biological process, and CC = cellular component). All the obsolete GO terms are under the nodes ""obsolete molecular function""  (GO:0008369),  ""obsolete cellular component"" (GO id GO:0008370), and ""obsolete biological process"" (GO:0008371).  Each of these GO ids has a group of GO ids as their direct children (nodes directly linked to but below the GO ids along the directed acyclic graph defined by GO)  with GO terms that were defined by GO but are deprecated in the current build. Data contained here are intended to allow users to map probe ids found in other Bioconductor data packages to GO terms using GO ids as the linkages."	GO	N
AnnInfo	Information file for source data	"This is a text file containing annotation element names that are used for annotation as keys and lists as values. Each list contains a short (a short description of the key), long (a long description of the key), src (a short name for the source such as LL (LocusLink)), and Y/N indicating whether the key is probe based. The text file will be used to generate the XML file and Rd files for data packages. "	NA	N
AFFY	Affymetrix identifier	Affymetrix identifier	NA	Y
PROBE	Generic identifier	A generic identifier for the target to be annotated	NA	Y
ASSOCIATION	The association between a GO term and the GO term of its parents	"This is an R environment (hash table like) object containing key and value pairs for the mappings between GO terms and its association with its parent GO terms (is a or part of the parent term). Keys can be accessed using ls(name) and values using get(key, name) or multiget(keys, name). Values are named vectors of length 1 or more depending on wither a given GO term has association with one or more parental GO terms. The name of the gives the GO id to which a given go id is associated either as a part of or is a relationship. GO terms do not have association with any parental GO terms are assigned a value NA. "	GO	N
ORGANISM	Name of the organism	This is a character string for the name of the organism of concern. The name of the organism can be viewed by typing the name of the binary file that will be loaded when the package is loaded by calling library(packageName)	NA	N
CHRLENGTHS	The total lengths of chromosomes	This is a named vector of integers for the lengths of chromosomes measured as the total number of base pairs. Names of integers indicate the chromosome number. Total lengths of chromosomes were derived from the Human Genome Project (http://genome.cse.ucsc.edu/goldenPath) by calculating the length of the sequence string. 	GP	N
DESCRIPTION	A short description of a probe	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe ids and descriptive information about the probe. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1. Probe ids that can not be mapped to descriptive information are assigned a value NA. "	YG	Y
ORF	Open Reading Frame id	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe ids and open reading frame ids used for yeasts. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1. Probe ids that can not be mapped to descriptive information are assigned a value NA."	YG	Y
ALIAS	Alia gene names 	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe ids and alia names used for yeasts. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Values are vectors of length 1 or more depending on whether a probe id can be mapped to one or more alia names. Probe ids that can not be mapped to descriptive information are assigned a value NA."	YG	Y
#HGID2LL#	Mappings between internal HomoloGeneIDs to LocusLink ids	This is an R environment object containing key and value pairs for the mappings between  #ORGANISM# internal HomologGeneIDs (keys) used by NCBI to represent sequences and the LocusLink ids (values) of genes of other organisms that have been identified to have homology relationships with the sequences represented by the HomologGeneIDs.  Values may be vectors of length 1 or greater depending on whether a HomologGeneID has been identified to have homology relationship with only one or more other organisms. Vector names are the scientific names of the species for which a homolgy relationship has been identified.  Mappings were obtained using data from NCBI (\url{ftp://ftp.ncbi.nih.gov/pub/HomoloGene/hmlg.ftp})	HG	N
LL2HGID	Mappings between LocusLink ids to internal HomoloGeneIDs	"This is an R environment (hash table like) object containing key and value pairs for the mappings between  LocusLink ids to internal HomologGeneIDs assigned to a sequence. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a LocusLink id can be mapped to only one or mor HomologGeneIds. Vector names are the scientific names of the organism the mapped HomologGeneId corresponds to.  "	HG	N
HGID	Mappings between probe ids and internal HomoloGeneIDS 	"This is an R environment (hash table like) object containing key and value pairs for the mappings between  probe identifiers (key) and internal HomoloGeneIDs (values). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) multiget(keys, name of the environment). Values may be vectors of length 1 or greater depending on whether a given probe identifier can be mapped to only one or more internal HomoloGeneIDs. NA is assigned to probe identifiers that can not be mapped to an internal HomoloGeneID at this time. Mappings were obtained using data from NCBI (\url{ftp://ftp.ncbi.nih.gov/pub/HomoloGene/hmlg.ftp}). This environment allows users to like probe ids to HomoloGeneIDs so that the homologus genes of probe ids can be explored using another data package named homology."	HG	Y
#HOMODATA#	Mappings between internal HomoloGeneIDs to homology data of the best match	"This is an environment (hash table ) object containing key and value pairs for the mappings between #ORGANISM# internal HomologGeneIDs (keys) representing a sequence and the data for the best matching sequences in other organisms represented by a list of homoData object(s). The list for a given internal HomologGeneID may have one to many homoData objects in the list depending on if homolgy relationships have been identified in only one or more other organism(s). A homoData object has slots for the name of the organism (homoOrg), LocusLInk id (homoLL), internal HomologGeneId (homoHGID), and GenBank accession number (homoACC) of the best matching sequence, type of similarity (homoType. B - reciprocal best best between three or more organisms, b - reciprocal best match between two organisms, and c - curated homology relattionship between two organisms) and percent of identity (homoPS) of the alignment between the matching sequences, and a url (homoURL) to the source if the relationship is a curated orthology. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) multiget(keys, name of the environment). Objects with homoType  = B or b will not have any value for homoURL and objects with homoType = c will not have any value for homoPS. The value of a given slot of an object can be accessed by using homoOrg(xxx) for the homoOrg slot of the homoData object xxx, for example. "	HG	N
ORGCODE	A named vector for organism code	A named vector with organism code number used by NCBI as the values and the scientific name of the corresponding organisms as the names.	HG	N
#HGID2HGID#	Mappings between internal HomoloGeneIDs of two organisms 	This is an R environment object containing key and value pairs for the mappings between  #ORGANISM# internal HomologGeneIDs (keys) used by NCBI to represent sequences and the internal HomoloGeneIDs (Values) representing sequences in other organisms that have been identified to have homology relationships with the sequences represented by the HomologGeneIDs.  Values are named vectors of length 1 or greater depending on whether a HomologGeneID has been identified to have homology relationship with only one or more other organisms Vector names are strings of organism scientific names.  Mappings were obtained using data from NCBI (\url{ftp://ftp.ncbi.nih.gov/pub/HomoloGene/hmlg.ftp})	HG	N
#CHRNUM#START	Mappings between LocusLink ids to gene transcription start location	"This is an R environment (hash table like) object containing key and value pairs for the mappings between LocusLink ids (Keys) and the transciption starting location for the gene on chromosome number #CHRNUM# corresponding to the LocusLink id (Values). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) multiget(keys, name of the environment). The starting positions for both the sense and antisense strand are number of base pairs measured from the p (5' end of the sense strand) to q (3' end of the sense strand) arms. Values for the antisense strand have a leading ""-"" sign (e. g. -1234567). Values are named vectors of length 1 derived from the smallest start value found for the LocusLink id. Names of chromosome location values can be ""Confident"" when the gene can be confidently placed on a chromosome and ""Unconfident"" otherwise (denoted by ""\_random"" in UCSC data). Mappings were derived from data provided by UCSC(\url{http://www.genome.ucsc.edu/goldenPath})"	GP	N
#CHRNUM#END	Mappings between LocusLink ids to gene transcription end location	"This is an R environment (hash table like) object containing key and value pairs for the mappings between LocusLink ids (Keys) and the transciption ending location for the gene on chromosome number #CHRNUM# corresponding to the LocusLink id (Values). Keys can be accessed using ls(name) and values using get(key, name) multiget(keys, name). The ending positions for both the sense and antisense strand are number of base pairs measured from the p (5' end of the sense strand) to q (3' end of the sense strand) arms. Values for the antisense strand have a leading ""-"" sign (e. g. -1234567). Values are named vectors of length 1 derived from the largest end value found for the LocusLink id. Names of chromosome location values can be ""Confident"" when the gene can be confidently placed on a chromosome and ""Unconfident"" otherwise (denoted by ""\_random"" in UCSC data). Mappings were derived from data provided by UCSC(\url{http://www.genome.ucsc.edu/goldenPath})"	GP	N
LOCUSID2CHR	Mappings between LocusLink ids to chromosome number the gene resides	"This is an R environment (hash table like) object containing key and value pairs for the mappings between LocusLink ids (Keys) and the chromosome number the gene resides (values). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) multiget(keys, name of the environment). Values are vectors of length 1 or mor depending on whether a give LocusLink id can be mapped to one or more chromosomes. Mappings were derived from data provided by UCSC(\url{http://www.genome.ucsc.edu/goldenPath})"	GP	N
#REPLACEME#	Mappings between two public repository ids	"This is an R environment (hash table like) object containing key and value pairs for the mappings between #KEY#  (Keys) and the #VALUE# (values). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) multiget(keys, name of the environment). Values are vectors of length 1 or more depending on whether #KEY# can be mapped to one or more #VALUE# .#OTHERS# Mappings were derived from data provided by LocusLink (\url{http://www.ncbi.nih.gov/LocusLink})"	LL	N
#ONETOONEMAN#	Mappings between keys and values	"This is an R environment (hash table like) object containing key and value pairs for the mappings between #KEY#  (Keys) and the #VALUE# (values). Keys can be accessed using ls(#ENVNAME#) and values using get(#KEY#, #ENVNAME#) or multiget(#KEY#s, #ENVNAME#). Values are vectors of length 1. Mappings were derived from data provided by #DATASOURCE#"	NA	N
#ONETOMANYMAN#	Mappings between keys and values	"This is an R environment (hash table like) object containing key and value pairs for the mappings between #KEY#  (Keys) and the #VALUE# (values). Keys can be accessed using ls(#ENVNAME#) and values using get(#KEY#, #ENVNAME#) or multiget(#KEY#s, #ENVNAME#). Values are vectors of length 1 or more depending on whether #KEY# can be mapped to one or more #VALUE# . Mappings were derived from data provided by #DATASOURCE#"	NA	N
IMAGE	Mappings between probe ids and IMAGE ids	"This is an R environment (hash table like) object containing key and value pairs for the mappings between probe identifiers (key) and IMAGE ids (value). Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget (keys, name of the environment). Values are vectors of length 1. NA is assigned to probe identifiers that can not be mapped to IMAGE ids. Mappings between probe ids and IMAGE ids are assumed to be provided by users. "	NA	Y
#SEQUENCE#	Chromosome sequence data	"This is an R environment (hash table like) object containing key and value pairs for the mappings between RefSeq ids (key) and sequence fragments (contigs) corresponding to the ids on #ORGANISM# #CHROMOSOME# (value). Keys can be accessed using ls(#PKGNAME##ENVNAME#) and values using lookUp(key, #PKGNAME#, #ENVNAME#). Values are vectors of length 1 or more depending on whether multiple RefSeq ids are used to reference the contigs on a given chromosome for a given built. Mappings between RefSeq ids and contigs were obtained from NCBI's Reference Sequence Project (\url{http://www.ncbi.nlm.nih.gov/RefSeq/}). "	REFSEQ	N
#CHROMSEQ#	Sequence for a chromosome	This is a single character string containing DNA sequence of #ORGANISM# #NUMBER#. #EXTRAINFO# The data were obtained from #DATASOURCE#	GP	N
#EXON#	Data for a given sequence	"This is an R environment (hash table like) object contianing a vector of geneLoc objects for exons on #ORGANISM#  #NUMBER# . Each geneLoc object has 5 slots for #PROBEID# id (probeId), chromosome number the exon is on (chrom), strand (strand), start location (startLoc), and end location (endLoc). Values for each slot can be accessed by typing (in R) ""slotName(objectName)"" (e. g. probeId(obj1), where obj1 is a geneLoc object).  #DATASOURCE#.  "	GP	N
CYTOLOC	Mappings between chromosomes and locations of cytobands on the chromosome	"This is an environment (hash table ) object containing key and value pairs for the mappings between chromosome numbers and the locations of cytobands on chromosoms. The mapped values are lists of named vectors. The names of lists are cytoband ids (e. g. qA2, ...). Each list contains a vector of two elements of integers for the starting and ending locations of the band on the chromosome defined by the key the lists mapped to. Names of the vectors indicate whether the value is for the starting or ending location.    "	GP	N
#HGID2GB#		This is an R environment object containing key and value pairs for the mappings between  #ORGANISM# internal HomologGeneIDs (keys) used by NCBI to represent sequences and the GenBank accession numbers (values) of genes of other organisms that have been identified to have homology relationships with the sequences represented by the HomologGeneIDs.  Values may be vectors of length 1 or greater depending on whether a HomologGeneID has been identified to have homology relationship with only one or more other organisms. Vector names are the scientific names of the species for which a homolgy relationship has been identified.  Mappings were obtained using data from NCBI (\url{ftp://ftp.ncbi.nih.gov/pub/HomoloGene/hmlg.ftp})		
#HGID2PS#		"This is an R environment object containing key and value pairs for the mappings between  #ORGANISM# internal HomologGeneIDs (keys) used by NCBI to represent sequences and the percent of identity (values) of best matching genes in other organisms that have been identified to have homology relationships with the sequences represented by the HomologGeneIDs.  Values may be vectors of length 1 or greater depending on whether a HomologGeneID has been identified to have homology relationship with only one or more other organisms. Vector names are strings of the code used by NCBI for the organism of concern, LocusLink id for the best matching gene, and the type of similarity separated by a "";"". Type of similarity can be B - reciprocal best best match between three or more organisms, b - reciprocal best match between two organisms, or c - curated homology relationship between two organisms. Values of vectors vary between percent values and urls depending on whether the type of similarities are B/b or c, respectively. Mappings were obtained using data from NCBI (\url{ftp://ftp.ncbi.nih.gov/pub/HomoloGene/hmlg.ftp})"		
REFSEQ	Mappings to RefSeq identifiers		LL	Y
